Mandich v. United States ( 2015 )


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  •    In the United States Court of Federal Claims
    No. 02-1222T
    (Consolidated with No. 05-18T)
    (Filed: November 6, 2015)
    **********************
    ROBERT A. MANDICH and
    CAROL J. MANDICH,          TEFRA; Settlement; Notice of
    Deficiency; Computational
    Plaintiffs, Adjustment; Affected Item; 26
    U.S.C. § 465; At Risk Limitation;
    v.                         26 U.S.C. § 469; Passive Activity
    Limitation; Doctrine of Variance
    THE UNITED STATES,
    Defendant.
    **********************
    Thomas E. Redding, Houston, TX, with whom was Sallie W. Gladney,
    Houston, TX, for plaintiffs.
    Benjamin C. King, United States Department of Justice, Tax Division,
    Washington, DC, with whom were Mary M. Abate, Assistant Chief, David I.
    Pincus, Chief, Court of Federal Claims Section, and Caroline D. Ciraolo,
    Principal Deputy Assistant Attorney General, for defendant.
    _________
    OPINION
    _________
    BRUGGINK, Judge.
    This is a suit for refund of federal income tax and interest. Taxpayers,
    Robert and Carol Mandich (“the Mandiches” or “taxpayers”), filed two suits
    here seeking refunds. The cases have been consolidated. Both cases involve
    the same settlement agreement between the Mandiches and the Internal
    Revenue Service (“IRS”) regarding their investment in the Greenberg Brothers
    Partnership #12, also known as Lone Wolf McQuade Associates (“LWM”),
    which was the subject of a Final Partnership Administrative Adjustments
    (“FPAA”) under the Tax Equity and Fiscal Responsibility Act of 1982
    (“TEFRA”). 26 U.S.C. §§ 6221-6233 (2012). Instead of participating in the
    LWM partnership proceeding, the Mandiches settled their partnership items
    with the IRS. Then the IRS made computational adjustments to the Mandiches
    taxes for the years at issue to implement the terms of the agreement. These
    adjustments resulted in a tax deficiency, which plaintiffs paid. In their first
    suit, filed on September 18, 2002, plaintiffs allege that the IRS was barred
    from disallowing certain carryover credits because it had not timely issued a
    notice of deficiency as required by statute. The carryover credits impact tax
    years 1984, 1990, 1991, 1992, 1993, 1994, and 1995. The second lawsuit,
    filed on January 6, 2005, asserts that the IRS disallowed the application of
    suspended losses for tax years 1993-1995 in violation of the terms of the
    settlement agreement. The Mandiches claim that proper application of the
    settlement agreement to their carryover credits and suspended losses entitles
    them to a refund of tax and interest paid in the amount of $219,685.76.1 The
    government contests plaintiffs’ allegations and stands by the adjustments
    calculated by the IRS in 2000.
    This was one of several Greenberg Brothers partnerships that were the
    subject of litigation in this court. Bush, et al. v. United States, 
    78 Fed. Cl. 76
    (2007), affd., 
    655 F.3d 1323
    (Fed. Cir. 2011) (“Bush I”), was selected as a test
    case for the purpose of resolving a TEFRA issue common to the Greenberg
    Brothers partnership cases, including this case, namely, whether the IRS
    needed to issue notices of deficiency before assessing taxes as a result of
    adjustments flowing from partner-level settlements of the audit of the
    partnership in question. The undersigned held that deficiencies assessed
    against the Bushes as a result of settlement of their at-risk amount was a
    computational adjustment for which no additional notice of deficiency was
    required because no partner-level factual determinations were necessary. 
    Id. at 81-82.
    Next, Judge George Miller construed the language of one of the
    settlement agreements and held that losses suspended under § 465 pursuant to
    the terms of the agreement were subject to the restrictions in § 469 on the use
    of passive losses. Bush v. United States, 
    84 Fed. Cl. 90
    (2008) (“Bush II”).
    The parties disagree about the effect of the Bush decisions on this case,
    however.
    1
    This is the amount that plaintiffs demand in their first amended complaint,
    which was filed on February 10, 2014, in the lead case after the cases were
    consolidated.
    2
    In addition to the complexities inherent in determining tax liabilities for
    several years involving inter-related questions of both credits and losses and
    multiple settlement agreements, the case is complicated by the fact that some
    of the credits to which taxpayers claim entitlement are traceable to pre-TEFRA
    partnerships and that the law concerning the interplay between §§ 465 and 469
    has arguably changed since Mr. Mandich first invested in LWM. As if these
    factors did not involve sufficient complexity, the parties’ arguments have
    changed over time.
    Both parties moved for summary judgment on what eventually became
    three distinct issues. The briefing has been extensive and there were two oral
    arguments. The matter is now ready for resolution. For the reasons set out
    below, we grant in part and deny in part both parties’ motions for summary
    judgment.
    BACKGROUND2
    I.     Tax Years 1984-1996
    From 1983 until 1995, Mr. Mandich was a limited partner in Lone Wolf
    McQuade. LWM was the subject of a partnership proceeding beginning in
    July of 1991 pursuant to TEFRA. During a TEFRA partnership proceeding,
    the IRS audits the partnership and makes certain partnership-level
    determinations, the impact of which flow through to the individual partners
    who are responsible for reporting those items on their individual income tax
    returns because the partnership is not a taxable entity. The Mandiches chose
    to opt out of the LWM partnership proceeding by settling with the IRS. See
    26 U.S.C. § 6224(c) (providing that a partner may settle his or her partnership
    items with the IRS through a binding agreement). On August 7, 1999, the IRS
    and the Mandiches executed the “Form 906 Closing Agreement on Final
    Determination Covering Specific Matters” (“Closing Agreement”) regarding
    LWM. In the Closing Agreement, the parties agreed to the following:
    1. No adjustment to the partnership items shall be made for the taxable
    years 1983 through 1995 for purposes of this settlement.
    2
    The facts are derived from the attachments to the parties’ cross-motions for
    summary judgment. Relevant disputed facts are noted in the background
    section.
    3
    2. The taxpayers are entitled to claim their distributive share of the
    partnership losses for 1983 through 1995 only to the extent they are at
    risk under I.R.C. § 465.
    3. The taxpayers’ amount at risk for 1983 through 1986 is their capital
    contribution to the partnership.
    4. The taxpayers’ capital contribution to the partnership is $100,000.
    5. Taxpayers’ qualified investment for computing investment tax credit
    is the amount at risk set forth in paragraph #4.
    6. The taxpayers are not at risk under I.R.C. § 465 for any partnership
    notes, entered into by the partnership to acquire rights in the motion
    picture Lone Wolf McQuade and Strange Invader, whether or not
    assumed by the taxpayers. Any losses disallowed under this agreement
    are suspended under I.R.C. § 465. Such suspended losses may be used
    to offset the taxpayers’ pro rata share of any income earned by the
    partnership and/or other income in accordance with the operation of
    I.R.C. § 465.
    ....
    8. To the extent the partnership earns net income the taxpayers’
    [amount] at risk will be increased in accordance with I.R.C. § 465.
    ....
    12. Any deficiency in tax determined under this agreement will be
    subject to adjustments arising from a carryback or carryforward from
    other taxable years of any loss, credit or other tax attribute as allowed
    by the Internal Revenue Code.
    Pls.’ Mot. Sum. J. Ex. E at 14-15. The agreement thus presumptively limited
    the amount of losses the Mandiches could claim with respect to LWM, as well
    as the amount at risk for purposes of calculating credits to $100,000, and it
    established the terms by which the amount at risk for calculating losses and
    credits could be increased in the future.
    4
    On May 22, 2000, the IRS sent two letters to the Mandiches that
    reflected adjustments the IRS made to their tax returns for 1984 through 1989
    in light of the Closing Agreement. Attached to each letter were IRS forms
    4549A-CG, 886-A, and others adjusting income, deductions, and, when
    applicable, credits. The first letter covered tax years 1983-1985, although
    1984 was the only year in which the calculations triggered a tax deficiency.
    The IRS disallowed LWM schedule E losses in excess of $100,000 in 1983,
    which corresponded to the capital contribution and amount at risk permitted
    in the LWM Closing Agreement. For 1984, the IRS disallowed $73,194 of
    LWM schedule E losses, which increased the Mandiches’ taxable income to
    $47,238. After computing the tax, applying a political contribution credit, a
    general business credit, a special fuels credit, and applying the alternative
    minimum tax, the IRS concluded that the Mandiches owed $7,869 in tax for
    1984. The IRS estimated the interest due on this amount to be approximately
    $34,000. The forms also reflected the disallowance of $66,885 of LWM
    schedule E losses in 1985, which did not change the amount of tax the
    Mandiches owed in that year. Plaintiffs paid the assessment.
    The second May 22, 2000 letter covered tax years 1986-1989. It
    provided that the IRS made no adjustments to the 1987 and 1988 returns but
    reduced the amount of carryover stemming from the investment credits. In the
    letter, the IRS stated the following:
    We have ordered your 1990 through 1996 returns. It appears
    that the credit shown on your 1989 account was used on these
    years. You may want to send us copies of your 1990 through
    1996 tax returns, as we may not have the documents any longer.
    If we are unable to secure copies of your returns, we will make
    adjustments from the information available.
    Pls.’ Mot. Sum. J. Ex. L at 100.
    At this point it becomes necessary to interject other background facts
    not directly related to the LWM partnership Closing Agreement in order to
    explain plaintiffs’ subsequent actions. The Mandiches had been invested in
    a number of partnerships other than LWM, some of which triggered earlier
    Tax Court litigation. Although the record is less than clear, there were at least
    two settlement agreements coming out of that litigation and at least one
    judgment of the Tax Court. Some documents relating to the Tax Court
    litigation are available for tax years 1982 to 1983, but neither party is able to
    5
    locate plaintiffs’ tax returns prior to 1984, and the Tax Court records are very
    limited. It is, however, undisputed that the net result of the litigation was that
    some credits were disallowed, although the parties disagree about the extent
    of that disallowance. The key point is that, with respect to the years at issue
    here, plaintiffs initially had not attempted to use whatever credits they believed
    survived the Tax Court litigation because their income, in their view, was
    offset sufficiently by LWM losses. The credits suddenly became relevant,
    again, after the LWM settlement, because it had the effect of reducing losses
    from $311,874 to $100,000 (unless the Mandiches could demonstrate an
    increased amount at risk). In plaintiffs’ view, they were able to utilize
    carryover credits from prior years, not withstanding the Tax Court litigation,
    in order to deflect the decrease in available losses attributable to LWM.
    In July of 2000, the taxpayers responded to the IRS’s adjustments to
    losses for 1983 through 1985. They disagreed with the IRS with respect to
    whether they were limited by the LWM Closing Agreement in the use of the
    approximately $200,000 in suspended losses. As a result, on July 25, 2000,
    they filed amended tax returns for 1993-1996, seeking a refund of $4,748 in
    1993, a refund of $2,826 in 1994, and a refund of $68,555 in 1995. The
    taxpayers’ proposed adjustments took into account the use of suspended losses
    and increases in the amount of investment tax credit available in 1995 due to
    changes in the corresponding amount at risk. See 
    id. Ex. F
    at 067-68.
    On July 27, 2000, the IRS sent another letter to the Mandiches, this one
    adjusting their taxes in 1990-1996. The taxpayers’ 1990-1996 tax returns had
    shown a carryover credit of $102,798.00. The forms accompanying the July
    27 IRS letter reflected that the IRS disallowed the investment tax credit
    carryover for each year because of adjustments made for previous years which
    had, in the view of the IRS examiner, reduced the investment credit to zero.
    After reviewing the 1983 through 1989 tax years, the examiner noted rather
    cryptically that, “cases and per information found[,] appeals disallowed
    research credit in 1982 and partnership adjustment in 83 and 84 reduced large
    amount of [carryover]. Only small amounts were created in 83-86 AP all of
    the credit is used in 1989 with no [carryover].” 
    Id. at Ex.
    N at 143. As has
    become apparent in briefing here, by concluding that taxes were due for 1982,
    the IRS examiner must have also taken the position that no credits could have
    survived the Tax Court litigation.
    Because the IRS concluded that the carryover losses had been fully
    depleted in 1989, on July 31, 2000, it assessed the following tax deficiencies:
    6
    $8,637 in tax and $10,284.20 in interest for 1990; $10,770 in tax and
    $10,645.59 in interest for 1991; $14,540 in tax and $12,297.76 in interest for
    1992; $17,691 in tax and $12,755.47 in interest for 1993; $21,509 in tax and
    $12,535.50 in interest for 1994; $14,685 in tax and $6,518.98 in interest for
    1995; and $4,932 in tax and $1,591.23 in interest for 1996. Plaintiffs paid the
    assessment.
    The government concedes that a notice of deficiency was not issued
    prior to the July 31, 2000 assessment. It takes the position that it was
    unnecessary for the IRS to issue a notice, however, because the agency had no
    need to question plaintiffs’ continued preservation of carryover credits until
    after the IRS had disallowed losses pursuant to the LWM Closing Agreement.
    In other words, defendant contends that the IRS was merely making
    computational adjustments when it applied the LWM Closing Agreement to
    taxpayers’ attempted use of credits in place of losses.
    On September 18, 2000, the IRS denied the Mandiches’ July 25, 2000
    request for refund based on the assertion of suspended losses. The IRS
    explained its conclusion as follows:
    Your claim is based on the view that you have an increase in
    capital. To allow the claims, you must provide verification of
    the increase in capital such as cancelled checks, cash vouchers
    and/or cash transactions. Investment credit was limited per the
    906 [Closing Agreement] and the amount allowed has been used
    in prior adjustments.
    
    Id. Ex. J
    at 084.
    Plaintiffs filed another round of amended tax returns (Form 1040X) and
    claim for refund (Form 843) on October 08, 2002, for tax years 1984, 1986,
    and 1990-1996, which the IRS denied.
    Prior Litigation Regarding Robert A. Mandich’s 1981-1983 Taxes
    The IRS examiner’s July 27, 2000 note concerning previous cases and
    appeals most likely referred to the Tax Court case involving Robert A. and
    7
    Marguerite Mandich.3 This prior litigation began in October of 1987 after the
    IRS sent a notice of adjustment to Robert and Marguerite Mandich for tax
    years 1982 and 1983. According to the IRS’ Examination Information Report,
    the deficiencies in 1982 resulted from adjustments that the IRS made to losses
    claimed for Mara Investment Company and for Summer Lovers Partnership,
    and the disallowance of investment and business energy credits attributable to
    Saxon Energy and Summer Lovers Partnership. The adjustments allowed an
    investment credit of $1,471. In total, the adjustments resulted in Robert and
    Marguerite owing $37,956 in taxes for 1982.
    For 1983, the IRS made an upward adjustment to Robert and
    Marguerite’s income by recognizing income from the IREX Partnership and
    disallowing losses from Mara Investment Company. However, these
    adjustments did not affect Robert and Marguerite’s ultimate tax liability for
    1983 because their income remained negative. The examiner’s work papers
    for 1983 contain the following note: “Two partnerships in which you are an
    investor, Summer Lovers Associates and Lone Wolf McQuade Associates, are
    currently under examination under TEFRA proceedings. Consequently, there
    may be additional adjustments to your 1983 return in connection with the on-
    going examinations.” Def.’s Cross-Mot. Sum. J. at A-62.
    In the work papers attached to the 1987 Examination Information
    Report, which explain the 1982 and 1983 adjustments, the IRS determined that
    a $15,038 “[i]nvestment tax credit from the Children’s Classics Recording
    promotion[,] which was claimed on [Robert and Marguerite’s] 1981 tax return
    and subsequently carried forward to [their] 1982 and 1983 returns, has been
    disallowed in full per the 1981 appeals settlement dated Jan 7, 1987.” 
    Id. at A-58.
    Similarly, the IRS disallowed a $19,814 research and development
    credit claimed by Robert and Marguerite for activities conducted by Cocoa,
    Ltd. The IRS auditor also explained that all credits generated by the Summer
    Lovers Partnership, which were shown in the amount of $4,593,978.00, were
    disallowed in any amount that exceeded income from the activity at issue.
    Finally, all carryforward or carryback Saxon Energy credits were also
    disallowed.
    3
    In 1982 and 1983, Robert A. Mandich was married to Marguerite, and they
    filed a joint tax return. Marguerite is not a party to this action. Mr. Mandich
    filed his taxes separately in 1984 and 1985. By 1986, Mr. Mandich began
    filing jointly with his current wife, Carol, who is a party to this suit.
    8
    Upon receiving the adjustment to their 1982 and 1983 tax returns,
    Robert and Marguerite filed suit in the Tax Court. That litigation was resolved
    in 1993 through settlement.
    Although the Tax Court did not retain many of the records from Robert
    and Marguerite’s suit regarding their 1982-1983 returns, it did keep the order
    reflecting how the case was resolved. Specifically regarding the Saxon Energy
    Credits, the Tax Court adopted the parties’ stipulated settlement on January 26,
    1993. Pursuant to the settlement, Marguerite and Robert Mandich agreed that
    the resolution of Schillinger v. Commissioner, 
    60 T.C.M. 1470
    (1990),
    would control and that the formula used in that case would apply to determine
    the proper adjustments to the Saxon Energy items. Def.’s Cross-Mot. Sum. J.
    at A-73. Additionally, the parties agreed to the following:
    If the Saxon Energy issues in the Controlling Case are resolved
    in a manner which affects the same issues in other years (e.g.,
    the availability of investment tax credit or energy credit
    carrybacks or carryforwards) the resolution will apply to
    petitioners’ other years as if the petitioners in this case were the
    same as the taxpayers in the Controlling Case.
    
    Id. at A-74.
    Robert and Carol Mandich entered into a Form 906 Closing Agreement
    with the IRS, dated May 13, 1993 (“1993 Closing Agreement”), settling their
    partnership issues with respect to Summer Lovers Associates. Specifically, the
    parties agreed to the following:
    WHEREAS taxpayers are limited partners in the partnership
    known as Summer Lovers Associates.
    WHEREAS taxpayers have claimed a deduction, in the amount
    of $55,287.00 for their distributive share of the loss claimed by
    Summer Lovers Associates for the taxable year ended December
    31, 1982.
    WHEREAS it is desirable for Federal income tax purposes to
    agree on certain matters pertaining to taxpayers[’] partnership
    interest.
    9
    Now it is hereby determined and agreed for Federal income tax
    purposes:
    1.      That the taxpayers[’] initial amount at risk is
    $50,000.00.
    2.      That the taxpayers are entitled to claim investment
    tax credit of $5,000.00 for 1982.
    3.      That the taxpayers are allowed to claim a loss
    from Summer Lovers Associates in 1982 in the
    amount of $50,000.00.
    4.      That the losses disallowed because they exceed
    the amount at risk will be carried forward in
    accordance with I.R.C. § 465.
    5.      To the extent the partnership earns net income
    after 1982, the at risk amount will be increased in
    accordance with I.R.C. § 465.
    6.      The taxpayers are not liable for any additions to
    tax with respect to their investment in Summer
    Lovers Associates.
    ....
    Pls.’ Resp. Ex. LL at 245-46. On May 27, 1993, the Tax Court entered a
    decision in Marguerite and Robert Mandich’s case adopting the parties’
    agreement recognizing a tax deficiency of $9,811.00 in 1982.
    While the suit involving tax years 1982 and 1983 awaited resolution in
    the Tax Court, the IRS continued to audit the taxpayers’ other returns. In
    1988, the IRS examined Mr. Mandich’s 1985 return and found “a $19,814.00
    Research Activities credit on form 6765 of your 1985 tax return as a
    carryforward from prior years. Since this credit (from Cocoa, Ltd.) was
    disallowed in full in your appeals settlement for your 1981 tax return, it is not
    allowable in 1985 or in any other tax year.” Def.’s Cross-Mot. Sum. J. at A-
    416. Also during this 1988 review, the IRS concluded that the taxpayers’ 1986
    10
    tax return did not appear to present sufficient audit potential and it was
    therefore accepted as filed.
    As described earlier, in 1991, the IRS issued an FPAA concerning the
    LWM partnership, which affected plaintiffs’ taxes from 1983 to 1995.
    Plaintiffs filed suit here on September 18, 2002, and again on January 6, 2005,
    claiming entitlement to refunds of taxes and penalties paid with respect to tax
    years 1984, and 1990-1995.
    DISCUSSION
    Over the course of four rounds of briefing and two oral arguments,
    three questions have come into focus. First, whether taxpayers may, in the
    absence of 26 U.S.C. § 469 but pursuant to § 465 and certain IRS Forms, use
    suspended losses to offset ordinary income for tax years 1993-1995. Both
    code sections provide for limitations on the use of losses. Section 469 limits
    the investor’s use of losses based on the characterization of his participation
    in the investment entity as either passive or non-passive. Section 465 limits
    the investor’s use of losses to the amount at risk in the activity. These code
    sections are typically applied together, but the parties agree that § 469 does not
    apply in the precise circumstances of this case. Second, whether the IRS
    performed a computational adjustment when it disallowed taxpayers’ carryover
    credits in years 1984 and 1990-1995, which were traceable to previous Tax
    Court cases and settlements. If this disallowance is not fairly characterized as
    a computational adjustment flowing from the LWM Closing Agreement, then
    the IRS was statutorily obligated to serve taxpayers with a notice of deficiency
    within 3 years, which would have triggered the taxpayers’ right to dispute the
    adjustment. The parties agree that the statute of limitations presently bars the
    IRS from issuing the notice of deficiency. Third, whether the IRS improperly
    disallowed all investment tax credits generated by Mr. Mandich’s investment
    in LWM rather than simply reduce the amount of credits to $10,000 per the
    terms of the LWM Closing Agreement. We address each issue separately.
    I.     Suspended Losses and Section 465
    Plaintiffs contend that they are entitled to refunds for 1993-1995 based
    on using losses from the LWM partnership that were disallowed for 1983-1986
    and suspended for future use pursuant to § 465 to offset non-LWM income
    they reported for 1993-1995.
    11
    On their original returns plaintiffs had reported net passive income from
    LWM of $11,167 for 1993, $10,092 for 1994 and $20,469 for 1995, which
    they claimed was offset by LWM passive losses in those years. On July 25,
    2000, plaintiffs filed Forms 1040X for 1993, 1994 and 1995, claiming, inter
    alia, deductions against other income traceable to the suspended losses of
    $11,167, $10,092 and $20,469. Plaintiffs’ computations of the refunds due for
    1993, 1994, and 1995, attributable solely to the deductions equal to the net
    income reported from LWM after their partial concession, are $4,555, $3,997
    and $8,106. The parties agree that the outcome turns on interpretation of the
    LWM Closing Agreement in light of applicable law.
    The LWM Closing Agreement contains three provisions directly
    bearing on the suspended loss claims:
    6. . . . . Any losses disallowed under this agreement are
    suspended under I.R.C. § 465. Suspended losses may be used
    to offset the taxpayers’ pro rata share of any income earned by
    the partnership and/or other income in accordance with the
    operation of I.R.C. § 465.
    8. To the extent the partnership earns net income the
    taxpayers’ at risk will be increased in accordance with I.R.C.
    § 465
    ....
    15. Any refund claim attributable to the operation of this
    agreement shall be deemed to be timely filed and shall be
    allowed if it is filed with the IRS within one year of the
    execution of this agreement by the Commissioner of Internal
    Revenue.
    Section 465 of the Internal Revenue Code describes how deductions are
    to be limited by the amount at risk in the following manner:
    (a) Limitation to the amount at risk.--
    (1) In general. In the case of --
    an individual . . .
    engaged in an activity to which this section
    applies, any loss from such activity for the taxable
    12
    year shall be allowed only to the extent of the
    aggregate amount with respect to which the
    taxpayer is at risk . . . for such activity at the close
    of the taxable year.
    (2) Deduction in succeeding year. Any loss
    from an activity to which this section applies not
    allowed under this section for the taxable year
    shall be treated as a deduction allocable to such
    activity in the first succeeding taxable year.
    ....
    (c) Activities to which section applies.
    (1) Types of activities. This section applies to
    any taxpayer engaged in the activity of
    (A) holding, producing, or distributing motion
    picture films . . . .
    (d) Definition of loss. For purposes of this section, the term
    “loss” means the excess of the deductions allowable under this
    chapter for the taxable year . . . and allocable to an activity to
    which this section applies over the income received or accrued
    by the taxpayer during the taxable year from such activity. . . .
    Currently, § 465 works in tandem with § 469. Section 469 provides that
    an individual may not deduct passive activity loss in excess of passive activity
    income. An activity is characterized as passive if it “involves the conduct of
    any trade or business . . . in which the taxpayer does not materially
    participate.” § 469(c). Any unused passive loss may be carried over to the
    next tax year in which the individual has excess passive income. In Bush II,
    Judge Miller held that § 469, which became effective on January 1, 1987,
    applied to the losses asserted there, with the result that plaintiffs were barred
    from using passive activity losses and credits unless they could be applied to
    passive activity 
    income. 84 Fed. Cl. at 95-96
    .
    In its opening brief, defendant argued that Bush II controlled the
    outcome here, namely, that LWM losses could only be deducted against
    passive income for 1993-1995, and not against other income. As the taxpayers
    here point out, however, the Tax Reform Act (“TRA”) of 1986 provided that
    its amendment to the passive loss and income provisions did not apply to “any
    loss, deduction, or credit carried to a taxable year beginning after December
    31, 1986, from a taxable year beginning before January 1, 1987.” Pub. L. No.
    99-514, § 501(c)(2), 100 Stat. 2085, 2241 (1986) (“Special Rule for
    13
    Carryovers”). Prior to the TRA, there had been no generally applicable
    limitation on a taxpayer’s ability to use losses based on their characterization
    as passive or non-passive. See Lowe v. Commissioner, 
    96 T.C.M. 502
    ,
    505 (2008).
    In its reply brief, defendant concedes that it was wrong: “Because of
    these exemptions [contained in the TRA,] any previously-disallowed LWM
    losses plaintiff[s] might be able to use in years after 1986 would not be subject
    to the passive loss limitation in § 469.” Def.’s Reply 2.4 It contends that the
    outcome is unchanged, however, because § 465, which limits the losses that
    can be claimed for a particular activity to the at-risk amount for that activity,
    still requires that previously disallowed losses from an activity must first be
    used to offset any income from that partnership activity in a subsequent year.
    In other words, the taxpayers’ previously-disallowed LWM losses first had to
    be used to offset their LWM income in 1993-1995. Then any deduction tied
    to the suspended losses in excess of LWM income would have to correspond
    with an increase in plaintiffs’ amount at risk. The parties agree that plaintiffs’
    LWM amount at risk did not increase in 1993-1995. Defendant contends
    therefore that, because the taxpayers’ at-risk amount with regard to LWM did
    not increase in those years, taxpayers can only use the previously-disallowed
    LWM losses to offset LWM income received in 1993-1995, and not to offset
    other income. This produces the same net result to plaintiffs’ tax liability as
    the method which plaintiffs originally used on their return.
    For 1993-1995, the taxpayers reported their LWM income as passive
    income pursuant to § 469, which was offset by their passive activity losses for
    those years. Defendant contends that using previously-disallowed LWM
    losses to offset LWM income would not reduce the taxpayers’ taxable income
    for those years, but only their passive income. This would remove LWM
    income from taxpayers’ passive income for those years and decrease the
    amount of passive losses they had to use and thereby increase the passive loss
    4
    As it further concedes, the applicable regulations make this explicit: “Section
    1.469-1(d)(2)(ix) of the regulations exempts from the operation of § 469 losses
    that were carried over from a pre-1987 year, pursuant to the carryover
    provisions in §§ 172, 613A, or 1212. Section 1.469-1(d)(2)(x) exempts from
    § 469 losses that were disallowed prior to 1987, pursuant to §§ 704, 1366, or
    465.” Def.’s Reply 2.
    14
    carryover to the following year. It would not, however, according to
    defendant, create a net loss that could be claimed as a refund.
    Defendant cites to proposed regulations that set out two ways in which
    deductions are allowable under § 465: 1) to the extent of income received from
    the activity in the taxable year; and 2) to the extent that the taxpayer is at risk
    if deductions exceed income. See Prop. Treas. Reg. §§ 1.465-2(a), 1.465-
    11(c). These proposed regulations were endorsed in Allen v. Commissioner,
    T.C. Memo. 1988-166, 
    1988 WL 34867
    *10-11 (1988). Defendant also cites
    commentators to the same effect. In Partnership Taxation, Willis, Pennell,
    Postlewaite, Thomas Reuters, 2015, ¶ 7.05, at 1, for example, the authors state
    that
    if a loss is not allowed for a particular year . . . with respect to
    a specified activity by reason of the at risk provisions, the loss
    carries over and reduces income or increases the loss from that
    activity in the following year . . . . If there were a second loss
    in the succeeding year . . . from that activity, the original . . . loss
    and the at risk limitation then would apply to the total of the two
    amounts. . . .
    . . . . The only requirement is that a loss not permitted to be
    deducted under the at risk rules must be carried over and
    deducted in a later year with respect to the operation of the same
    activity. The disallowed loss may be deducted with respect to
    the same activity in a later year against either: (1) the realization
    of a profit, or (2) an increase in the amount at risk through
    contribution of new capital or an increase in at risk partnership
    liabilities.
    The net result, according to defendant, is that “The previously
    disallowed LWM losses can be used to offset plaintiffs’ non-LWM income
    only to the extent those losses exceed the amount of LWM income in that year,
    and to the extent that plaintiffs’ at risk amount was increased beyond the
    amount of income received.” Def.’s Reply 5. Because taxpayers do not allege
    that their amount at risk increased in those years, the excess losses would have
    to be carried over again and could not be applied to taxpayers’ other income.
    15
    Part of defendant’s reasoning is that, although § 469 did not take effect
    until after the suspended losses were generated, it does apply to the calculation
    of income and losses generated in 1993-1995. In those years, the LWM
    income that taxpayers received was reported as passive activity income.
    According to defendant, plaintiffs elected to offset their LWM passive activity
    income with passive losses from other sources. Defendant argues that the
    taxpayers cannot take a deduction pursuant to § 469 and at the same time use
    the income from the § 469 calculation to access losses suspended pursuant to
    § 465. According to defendant, plaintiffs are entitled to one deduction under
    either § 469 or § 465 based on the income, not two deductions operating under
    § 465 and § 469 separately.
    Plaintiffs disagree with defendant’s explanation of how § 465 operates
    in the absence of § 469. They argue that the standard IRS Forms 6198, 8582,
    and Schedule E of the Form 1040 permitted them to apply their suspended
    losses against other non-LWM income in 1993-1995. According to plaintiffs,
    they began in 19935 with suspended losses totaling $227,709. In 1993, LWM
    earned income of $11,167. This LWM income, per the taxpayers, frees up a
    corresponding amount of suspended losses and is reported on lines 1 and 5 of
    Form 6198 (At-Risk Limitations) as negative $216,542. All other lines on
    Form 6198 are either not applicable or zero. Even though plaintiffs’ 1993
    LWM income has been cancelled out by the suspended loss for purposes of
    Form 6198, the taxpayers contend that this effect is only for purposes of Form
    6198. Plaintiffs explain that “[n]either § 465, the regulations, nor the Form
    6198 instructions provide how the component parts ($11,167 of income and
    the allowable $11,167 of previously suspended ‘at-risk’ loss) are actually
    reported on Schedule E and then on Form 1040.” Pls.’ Suppl. Br. & Resp. to
    Def.’s Suppl. Br. 3. Instead, the taxpayers point to the 1993 Instructions for
    Form 6198, which provided, “[i]f the loss on line 5, Part I, is equal to or less
    than the amount on line 20, report the items in Part I in full on your return,
    subject to any other limitations such as the passive activity and capital loss
    limitations. Follow the instructions for your tax return.” 
    Id. Ex. UU
    at 7.
    Plaintiffs next turn to Form 8582 (Passive Activity Loss Limitations),
    which the taxpayers filed in 1993. See 
    id. Ex. VV.
    On this form, plaintiffs
    5
    Plaintiffs’ argument is the same for all three tax years at issues, 1993-1995,
    and while we only lay out the facts for 1993, our analysis for all three years is
    likewise the same.
    16
    report $16,976 of passive income, including $11,167 of income generated by
    LWM in that year. This form also shows that, in 1993, plaintiffs had $37,430
    in passive losses6 and carryover passive losses of $101,582. These passive
    losses were more than sufficient to offset the passive income. The result of the
    calculation suggested by Form 8582 is that the Mandiches have $16,976 of
    losses for use in 1993, $11,167 of which are allowable because of the passive
    LWM income that was also used to free up the suspended losses pursuant to
    Form 6198.
    According to the taxpayers, this duplication is permissible because the
    1993 Instructions for Schedule E direct that, “[i]f you have losses or
    deductions from a prior year that you could not deduct because of the at-risk
    or basis rules, and the amounts are now deductible, do not combine the prior
    year amounts with any current year amounts to arrive at a net figure to report
    on Schedule E. Instead, report the prior year amounts and the current year
    amounts on separate lines of Schedule E.” 
    Id. at Ex.
    BBB E-4. Accordingly,
    the taxpayers assert that their Schedule E line 27(g) (Passive loss allowed)
    would remain allowable and unchanged but that they would also be entitled to
    add $11,167 on line 27(i) (Nonpassive loss from Schedule K-1). This would
    change line 30 from negative $15,711 to negative $26,878, reflecting the
    additional $11,167 in deductible losses. The result in line 31 is a reduction of
    total partnership and S corporation income from $30,983 to $19,816. In this
    manner, the taxpayers assert that the tax forms support their interpretation of
    § 465 as permitting an additional deduction traceable to their LWM losses that
    were suspended by the terms of the LWM Closing Agreement.7
    While a rigid adherence to the tax forms may produce the result that the
    taxpayers seek, the forms simply represent guidance and do not supersede the
    statute. Additionally, the forms were not written to address the precise
    circumstance that is identified in this case, namely, when § 469 does not apply
    to the suspended losses but § 465 does and the income generated is subject to
    both code sections. We are therefore unpersuaded by plaintiffs’ reliance on the
    6
    These passive losses are traceable to various activities other than LWM.
    7
    On September 21, 2015, plaintiffs filed, without leave of the court, an
    additional supplemental brief that cited Treas. Reg. § 1.469-2T in support of
    their position. This regulation does not aid plaintiffs’ theory of duplication but
    stands for the proposition that losses, which arose before 1987 and were
    suspended, “must be accounted for separately.” Treas. Reg. § 1.469-2T.
    17
    tax forms to manufacture duplicated losses not allowed by the tax code. In the
    absence of an increase in the amount at risk, § 465 bars any deduction tied to
    the suspended losses in excess of LWM income.
    Defendant has convinced us that § 465 operates to limit plaintiffs’
    ability to use the suspended losses beyond their application to offset income
    from that activity in the current year. Any exception to this limitation would
    be the result of an increase in plaintiffs’ amount at risk. Because there was no
    such increase in the amount at risk, plaintiffs may not use the suspended losses
    to offset income from sources other than the activity. Although under this
    ruling plaintiffs would be able to shift which pool of losses are applied to
    offset their LWM income from the passive loss pool to the suspended loss
    pool, the bottom line does not change. Either way, their income of $11,167 in
    1993, $10,092 in 1994, and $20,469 in 1995 is offset by losses and thus not
    taxed. Because plaintiffs’ ultimate tax liability remains unchanged, we deny
    plaintiffs’ request for refund in this respect.
    II.    Carryover Credits and Computational Adjustments
    Mr. Mandich’s original 1983 return claimed no credits against 1983
    taxes, but it contained schedules showing available carryover credits of
    $104,572, consisting of carryovers from 1982; $29,206 from an investment tax
    credit, an energy investment credit of $24,000, and an increasing energy credit
    of $19,814, plus a new (in 1983) investment tax credit of $31,552, of which
    $31,188 was from Mr. Mandich’s investment in LWM. Pursuant to the LWM
    Closing Agreement, the allowable LWM tax credit was limited to $10,000.
    In implementing the LWM Closing Agreement, the IRS, when
    calculating the tax credit carryovers from 1983 to make adjustments to
    taxpayers’ returns for 1984 and 1990-1995, disallowed all prior credits which
    the taxpayers had attempted to carryover from 1983, other than a $364 credit,
    and a new (to 1984) credit of $788. If the IRS had allowed the other carryover
    credits plaintiffs claimed, the Mandiches could have offset the taxes assessed
    pursuant to the LWM Closing Agreement’s disallowance of over $200,000 in
    LWM losses. Instead of applying the carryover credits against plaintiffs’
    increased tax bills in years 1984 and 1990-1995, the IRS disallowed all of the
    non-LWM credits. It did this in 2000, at a time when those returns were
    otherwise not accessible to the IRS to make adjustments and assessments.
    18
    Specifically, under Internal Revenue Code §§ 6212 and 6213, which are
    contained in sub-chapter B “Deficiency Procedures,” the IRS must mail a
    notice of deficiency to the taxpayer before assessing any levy or pursuing a
    proceeding in Tax Court. The IRS has a limited period of time, three years
    from the date the taxpayer filed its return, in which to mail a notice of
    deficiency and begin a proceeding against the taxpayer. § 6501(a). There is
    an exception, however, carved out under TEFRA for partnership adjustments
    made pursuant to an FPAA or, in this case, the implementation of a closing
    agreement accepting the results of the FPAA. § 6213(h)(3) (referring to §
    6230). Section 6230(a) provides the following:
    (a) Coordination with deficiency proceedings.--
    (1) In general.--Except as provided in paragraph (2) or
    (3), subchapter B [“Deficiency Procedures”] of this
    chapter shall not apply to the assessment or collection of
    any computational adjustment.
    (2) Deficiency proceedings to apply in certain cases.--
    (A) Subchapter B shall apply to any deficiency
    attributable to
    (i) affected items which require partner
    level determinations (other than penalties,
    additions to tax, and additional amounts
    that relate to adjustments to partnership
    items), or
    (ii) items which have become
    nonpartnership items (other than by reason
    of section 6231(b)(1)(C)) and are
    described in section 6231(e)(1)(B).
    (B) Subchapter B shall be applied separately with
    respect to each deficiency described in
    subparagraph (A) attributable to each partnership.
    (C) Notwithstanding any other law or rule of law,
    any notice or proceeding under subchapter B with
    respect to a deficiency described in this paragraph
    shall not preclude or be precluded by any other
    notice, proceeding, or determination with respect
    to a partner’s tax liability for a taxable year.
    § 6230(a) (emphasis supplied).
    19
    The code further defines “computational adjustment” as “the change in
    the tax liability of a partner which properly reflects the treatment . . . of a
    partnership item. All adjustments required to apply the results of a
    [partnership] proceeding . . . to an indirect partner shall be treated as
    computational adjustments.” § 6231(a)(6). Pursuant to § 6230, computational
    adjustments may be made to both partnership items and to some affected items.
    An affected item is “any item to the extent such item is affected by a
    partnership item.” § 6231(a)(5); see Keener v. United States, 
    76 Fed. Cl. 455
    ,
    460-61 (2007). Treasury Regulation § 301.6231(a)(5)-1(a), further provides:
    “The term ‘affected item’ . . . . includes items unrelated to the items reflected
    on the partnership return (for example, an item, such as the threshold for the
    medical expense deduction under section 213, that varies if there is a change
    in an individual partner’s adjusted gross income).” An affected item may be
    altered by a computational adjustment if the adjustment does not require
    individualized, i.e., partner level, factual determinations. 26 U.S.C. §
    6230(a)(2)(A)(i); see Bush v. United States, 
    655 F.3d 1323
    , 1330-31 (Fed. Cir.
    2011) ((“[A]ssessments are ‘computational adjustments’ when they require ‘no
    individualized factual determinations’ as to the correctness of the original
    partnership items or ‘any other factual matters such as the state of mind of the
    taxpayer upon filing.’”) (quoting Olson v. United States, 
    172 F.3d 1311
    , 1318
    (Fed. Cir. 1999))). The net result is that the IRS is authorized to make
    computational adjustments to items affected by partnership items so long as
    the adjustment does not require the IRS examiner to make a partner-level
    factual determination.
    Both parties agree that only $31,188 of the $104,572 cache of tax
    credits was originally generated in 1983 by Mr. Mandich’s investment in
    LWM and is therefore subject to a computational adjustment to effectuate the
    terms of the LWM Closing Agreement.8 Therefore, as taxpayers correctly
    point out, in the abstract, the IRS’s disallowance of the taxpayers’ claimed
    carryover credits from 1983, totaling $73,384, bears no necessary connection
    to the results of the LWM Closing Agreement. The parties diverge, however,
    8
    While the taxpayers do not dispute the fact that the credit created by their
    investment in LWM is subject to computational adjustment, the taxpayers do
    take issue with the IRS’s alleged disallowance of all of that credit, including
    $10,000, which plaintiffs assert was preserved by the LWM Closing
    Agreement.
    20
    in their views about whether these pre-1983 carryover credits may be adjusted
    as affected items.
    According to plaintiffs the IRS must accept the $73,384 figure as
    reported on their tax return and cannot challenge whether those credits were
    legitimate at the times they were claimed and repeatedly carried over from
    1983 into following years.9 Plaintiffs’ argument is this: any tax liability
    resulting from the disallowance of pre-1983 credit carryovers that was
    unrelated to LWM could not be assessed as a computational adjustment, first,
    because TEFRA did not go into effect until 1983, and, second, because the
    non-LWM credit carryovers are partner-level affected items requiring partner-
    level determinations and hence a deficiency notice. In effect, according to the
    taxpayers, the maximum disallowance which could have been made was
    $21,188;10 the critical adjustments were non-TEFRA adjustments and hence
    were invalid because they were made without a deficiency notice.
    The government disagrees. It claims that the $73,384 in carryover tax
    credits was disallowed in previous Tax Court proceedings and through earlier
    Tax Court settlements, and thus the IRS was merely giving effect to these
    determinations by way of computational adjustments when it implemented the
    LWM Closing Agreement. In order to support its claim, defendant points to
    the 1993 Tax Court decision, which it reads as disallowing all tax credits
    claimed for 1982 pursuant to stipulation. The sparse Tax Court record
    produced by the government in this case includes a stipulation and order
    whereby taxpayers agreed that the result to their Saxon Energy credits would
    be dictated by the resolution of Schillinger v. Commissioner, 
    60 T.C.M. 1470
    (1990). It also included the taxpayers’ closing agreement that settled
    9
    Although the IRS presumably could have challenged the credits prior to the
    LWM Closing Agreement, it did not do so. Instead, it waited until after the
    Mandiches’ LWM partnership items were settled in 1999, and only then after
    plaintiffs attempted to use the credits. Then it became clear the IRS took a
    different view of the Closing Agreement in terms of how the taxpayers could
    apply unused credits. In that sense, they would appear to be partner-level
    items not protected by the “computational adjustment” exception.
    10
    This $21,188 figure is the balance remaining once the $10,000 LWM
    investment credited permitted pursuant to the terms of the LWM Closing
    Agreement is subtracted from the $31,188 LWM investment credit originally
    claimed by the Mandiches.
    21
    their partnership issues regarding Summer Lovers Associates. Pursuant to that
    closing agreement, the taxpayers’ Summer Lovers amount at risk, credits, and
    losses were reduced. At the close of the Tax Court case, the Mandiches were
    left with a tax deficiency of $9,811. According to the government, the only
    way that the Mandiches would have owed a tax bill at the end of that case was
    if all of their credits had been disallowed. This conclusion, per defendant, is
    consistent with the 1987 Examination Information Report and accompanying
    work papers, which shows that the IRS intended to disallow the Saxon Energy
    credits, the Summer Lovers credits, the Children’s Classics Recording credit,
    and the Cocoa Ltd. credits. Thus, according to defendant, all partner-level
    factual determinations necessary to disallow all carryover credits were already
    made by the Tax Court, and therefore the IRS was simply making a
    computational adjustment when it disallowed the credits in 2000.
    The problem with this evidence, according to plaintiffs, is that it is
    incomplete and is inconsistent with defendant’s ultimate conclusion that no
    credits survived the judgment of the Tax Court. Specifically, plaintiffs take
    issue with the government’s reliance on the Examination Information Report
    and work papers, because the adjustments proposed therein differ significantly
    from the result in the Tax Court. Taxpayers accurately point out that the
    examination report proposed a deficiency of $37,957 with penalties of $12,898
    for 1982. By contrast, the Tax Court determined that the taxpayers owed
    $9,811 in taxes for 1982 plus penalties that amounted to approximately $5,000.
    Additionally, the examination report disallowed all of the taxpayers’ $55,000
    loss incurred in the Summer Lovers partnership, while the Summer Lovers
    closing agreement accepted by the Tax Court permitted $50,000 of loss to be
    used by the taxpayers. Finally, plaintiffs contend that the only evidence that
    defendant has provided to support its assertion that credits traceable to
    Children’s Classics Recordings and Cocoa Ltd. were disallowed in their
    entirety is a proposal for settlement contained within the documents attached
    to the Examination Information Report.
    Plaintiffs are correct that the record contains no evidence of how and
    when the credits from Cocoa Ltd. and Children’s Classic Recordings were
    formally and finally disallowed. Furthermore, while we are persuaded from
    the Tax Court record that the Saxon Energy credits were disallowed, we are
    unable to match up the value that was disallowed with an identifiable part of
    the credits that were disallowed in the present adjustment. Moreover, the
    government’s assertion that no credits survived the conclusion of the Tax
    Court case is squarely contradicted by the fact that the taxpayers retained a
    22
    $5,000 tax credit pursuant to the terms of the Summer Lovers closing
    agreement, which was accepted by the Tax Court. There are significant
    limitations in the evidence before us such that we cannot trace the wholesale
    disallowance of the bulk of plaintiffs’ pre-1983 carryover credits by
    computational adjustment in 2000 to specific instances in which each credit
    was previously disallowed by a competent authority.
    The point is this: on the present record we would have to make partner-
    level factual determinations in order to untangle the mess of credits and
    previous legal proceedings to arrive at the conclusion that all pre-1983
    carryover credits were previously disallowed.
    Although in principal we do not disagree with the government’s
    argument that applying the judgment of another court could be a computational
    adjustment to an affected item if the adjustment involved no partner-level
    factual determinations, we cannot reach that holding in this case because
    plaintiffs have shown that the IRS’s adjustment to plaintiffs’ carryover credits
    were not free from individual factual determinations. By showing that the
    adjustment was not merely computational, plaintiffs have rebutted the
    presumption of correctness. There is thus a failure of proof to support the
    government’s argument that it did not need to file a notice of deficiency.11 If
    the government had preserved a more complete record, we might have been
    able to reach a different conclusion.
    Because the IRS’s disallowance of plaintiffs’ pre-1983 carryover credits
    was not a computational adjustment, we hold that the disallowance was
    unlawful in the absence of a notice of deficiency. The time in which the IRS
    could have issued a notice of deficiency has long since passed. Plaintiffs are
    entitled to the use of $73,384 in credits to offset their tax deficiency computed
    as a result of the LWM Closing Agreement.12
    11
    Neither party has suggested that this is a triable issue of fact. The
    government has not suggested that it could offer live testimony on this issue,
    and we are satisfied that no further documentary evidence can be adduced
    beyond what the parties have furnished the court.
    12
    Due to this holding, we find it unnecessary to address plaintiffs’ alternative
    argument that the TEFRA exception to the deficiency procedures does not
    apply to pre-TEFRA items.
    23
    III.    Credits Attributable to LWM
    The carryover credits are not the only credits that plaintiffs claim should
    have been available to offset their tax liability. The taxpayers assert that,
    under the terms of the Closing Agreement, they were entitled to a $10,000 tax
    credit for their investment in LWM. Plaintiffs rely on two provisions of the
    LWM Closing Agreement: “4. The taxpayers’ capital contribution to the
    partnership is $100,000. 5. Taxpayers’ qualified investment for computing
    investment tax credit is the amount at risk set forth in paragraph #4.” Pls.’
    Mot. Sum. J. Ex. E at 14-15. In the year at issue, the investment credit was
    equal to 10% of the qualified investment.13 Thus, plaintiffs assert that they
    were entitled to a credit of $10,000, which is 10% of their $100,000 qualified
    investment and amount at risk. Plaintiffs contend that the IRS’s computational
    adjustment did not factor in this $10,000 credit and instead disallowed the
    entire original LWM credit of $31,188.
    The government’s rationale for opposing plaintiffs’ request for a refund
    based on this assertion has morphed. First, defendant claimed that the IRS had
    taken the $10,000 LWM investment credit into account while making the
    computational adjustment. Then, defendant conceded that it could not point
    to any evidence that the IRS had, in its computational adjustment, applied the
    $10,000 credit against plaintiffs’ tax deficiency, but defendant raised two
    additional arguments. First, it argued that plaintiffs had not carried the burden
    of proof with respect to their entitlement to the $10,000 credit. Second, it
    asserted that plaintiffs’ claimed entitlement to the $10,000 LWM credit
    substantially varied from their initial administrative claim for refund.
    As to the asserted failure of proof, defendant contends that plaintiffs
    have satisfied neither their burden of going forward nor their burden of
    persuasion with respect to the $10,000 investment credit because they did not
    produce evidence to show that the original $31,188 was attributable to LWM
    and thus that $10,000 of that credit should have been preserved according to
    the terms of th LWM Closing Agreement. Defendant cites Albemarle Corp.
    v. United States, for the following:
    13
    The parties do not dispute that “the allowable 1983 [investment tax] credit
    from the LWM Settlement would have been $10,000.” Pls.’ Am. Compl. ¶ 13;
    Def.’s Answer to Pls.’ Am. Compl. ¶ 13.
    24
    [T]o rebut the presumption of the Commissioner’s correctness,
    “the taxpayer must come forward with enough evidence to
    support a finding contrary to the Commissioner’s
    determination.” Bubble Room, Inc. v. United States, 159 F.3d
    [553], 561 [(Fed. Cir. 1998)]. Stated otherwise, to overcome the
    presumption, the taxpayer has the burden of presenting
    “substantial evidence as to the wrongfulness of the
    Commissioner’s determination.” KFOX, Inc. v. United States,
    
    206 Ct. Cl. 143
    , 151-152, 
    510 F.2d 1365
    , 1369 (1975);
    Arrington v. United States, 
    34 Fed. Cl. 144
    , 147 (1995), aff’d,
    
    108 F.3d 1393
    (Fed. Cir. 1997). The burden imposed on a
    plaintiff is both the burden of going forward and the burden of
    persuasion. Thus, a plaintiff first must come forward with
    enough evidence to support a finding contrary to the
    Commissioner’s determination. See Transamerica Corp. v.
    United States, 902 F.2d [1540] 1543 [(Fed. Cir. 1990)]; Danville
    Plywood Corp. v. United States, 899 F.2d [3,] 7-8 [(Fed. Cir.
    1990)]; Arrington v. United 
    States, 34 Fed. Cl. at 147
    .
    
    118 Fed. Cl. 549
    , 562 (2014), aff’d, 
    797 F.3d 1011
    (Fed. Cir. 2015).
    Defendant asserts that plaintiffs have not produced any evidence in this case
    to overcome the presumption of correctness and establish that the original
    disallowance of the full $31,188 credit was incorrect. According to defendant,
    the IRS work papers accompanying the adjustment do not identify the entity
    or entities that generated the $31,188 credit that was disallowed. In the
    absence of evidence that proves that all of the original $31,188 credit was
    attributable to LWM, defendant asserts that plaintiffs cannot establish that they
    are entitled to a $10,000 portion of that credit under the LWM Closing
    Agreement.
    Plaintiffs respond by referencing § 6230(a), which limits computational
    adjustments, in the absence of a notice of deficiency, to partnership items or
    affected items that do not require partner-level factual determinations.
    According to plaintiffs, the $31,188 investment credit was either known to be
    a LWM partnership item that could be disallowed by computational adjustment
    without a notice of deficiency or it was an affected item and, in the absence of
    evidence linking the entire credit to LWM, the IRS auditor made a partner-
    level factual determination to disallow the entire credit without first issuing the
    requisite notice of deficiency. Plaintiffs argue that, if the government is
    correct that there was no evidence that the entire $31,188 credit corresponded
    25
    to its original investment of $311,874 in LWM, and the disallowance of this
    credit was not made in an effort to implement the terms of the LWM Closing
    Agreement, which reduced plaintiffs’ LWM amount at risk from $311,874 to
    $100,000, then any adjustment, by definition, would require a partner-level
    factual determination and was therefore improper without a notice of
    deficiency.
    Plaintiffs are correct that the government cannot have it both ways.
    Defendant cannot claim that the IRS’s actions were procedurally sound in the
    past (i.e., did not trigger the notice of deficiency that is necessary when the
    adjustment requires partner-level factual determinations) and now assert that
    there is not enough evidence to conclude that the $31,188 credit was
    attributable to LWM. Either the IRS had sufficient evidence at the time of the
    adjustment to conclude that the $31,188 credit was a partnership item
    attributable to the taxpayers’ investment in LWM, in which case a
    computational adjustment was appropriate, or the IRS did not have sufficient
    evidence to conclude that the credit was entirely attributable to LWM but made
    a partner-level factual determination and fully disallowed the credit, an action
    which should have been preceded by a notice of deficiency. In this case, the
    fact that the IRS fully disallowed the credit points to the IRS’s understanding,
    at the time, that the credit was attributable to LWM. This follows logically
    from the documentation the taxpayers provided to the IRS and the figures that
    match up if the $31,188 credit was originally derived by computing 10% of
    $311,874.
    The question thus becomes, why did the IRS examiner not make a
    computational adjustment to implement the terms of the LWM Closing
    Agreement that permitted $10,000 of the $31,188 credit and disallow the
    remaining $21,188? The government has not provided a rationale for why the
    full amount of credit was disallowed. In fact, defendant agrees that, under the
    terms of the LWM Closing Agreement, a $10,000 credit was allowable. Def.’s
    Answer to Pls.’ Am. Compl. ¶¶ 13, 49. The only possible conclusion is that
    the IRS made a mathematical error that resulted, improperly, in the full
    disallowance of the LWM investment credit. We are satisfied that plaintiffs
    are entitled to this $10,000 investment credit to offset their tax liability.
    Defendant, however, raises one last bar to plaintiffs’ recovery. It
    asserts for the first time in its June 16, 2015 supplemental brief the defense of
    substantial variance.
    26
    The doctrine of substantial variance is rooted in the government’s
    limitation on its waiver of sovereign immunity made in 26 U.S.C. § 7422(a)
    and the regulatory requirement that the claim for refund of tax “must set forth
    in detail each ground upon which a credit or refund is claimed and facts
    sufficient to apprise the Commissioner of the exact basis thereof.” Treas. Reg.
    § 301.6402-2(b)(1). “Accordingly, new claims or theories raised subsequent
    to the initial refund claim are not permitted where they substantially vary from
    the theories initially raised in the original claim for refund.” Cencast Servs.,
    L.P. v. United States, 
    729 F.3d 1352
    , 1367 (Fed. Cir. 2013) (citing and
    applying 26 U.S.C. § 7422(a)).
    According to defendant, plaintiffs’ administrative claim did not alert the
    IRS to the issue of whether the $10,000 investment credit had been improperly
    disallowed. Plaintiffs’ administrative claim states in relevant part:
    1.        The settlement entered into by Closing Agreement
    provided there was no change to partnership items, but agreed
    that for purposes of determining the taxpayers’ correct tax
    liability for every partnership year from inception to termination
    (i) the taxpayers’ amount at risk regarding their Partnership
    investment would be determined based on several factors set
    forth in the agreement, (ii) “any deficiency in tax determined
    under this agreement will be subject to adjustments arising from
    a carryback or carryforward from other taxable years of loss,
    credit or other tax attributable as allowed by the Internal
    Revenue Code, . . . .
    7. The same grounds stated above apply to the assessments
    that were made based on the IRS’ determination of adjustments
    or carryovers or carrybacks as affected items under TEFRA
    arising from the settlement years.
    Pls.’ Mot. Sum. J. Ex. O at 152-53. Defendant asserts that the $10,000 credit
    issue is not evident in the administrative claim, specifically in paragraph 7,
    because it “is not based on any IRS adjustment of any credit carryover utilized
    on plaintiffs’ 1984 return.” Def.’s Suppl Br. 15. Because plaintiffs did not
    clearly set forth their entitlement to the $10,000 LWM investment credit
    during the administrative stage, defendant concludes that their present pursuit
    fatally varies from their original claim.
    27
    In response, plaintiffs assert that the carryover credit grounds, of which
    the $10,000 LWM credit is one part, is expressly contained in the
    administrative claims. According to plaintiffs, the doctrine of substantial
    variance is not a bar for an issue that is “comprised within the general
    language of the claim.” Ottawa Silica Co. v. United States, 
    699 F.2d 1124
    ,
    1138 (Fed. Cir. 1983).
    We agree. There is ample evidence to suggest that the $10,000 LWM
    credit issue was included in the general language of plaintiffs’ original
    administrative claim, the original complaints in these two case,14 and in the
    amended complaint in the lead case.15 Specifically, paragraph one of
    plaintiffs’ administrative claim relies on the terms of the Closing Agreement
    to establish the proper treatment of partnership items and invokes the Internal
    Revenue Code to apply in the event that any loss, credit, or other tax may apply
    against any deficiency determined in the adjustment. Likewise, paragraph
    seven alerts the IRS to potential issues with adjustments that were made to
    carryover and carryback credits. As originally claimed, the $10,000 credit was
    part of a $31,188 credit that was not used in 1984 but carried forward. We
    cannot agree with defendant that the use of the terms “carryovers and
    carrybacks” do not embrace the $10,000 credit. Plaintiffs’ administrative
    claim put the government on notice of the Mandiches’ challenge to the
    computational adjustment made to credit carryovers and carrybacks. The
    doctrine of variance, thus, does not bar plaintiffs’ recovery on this issue.
    Plaintiffs are owed a refund for the $10,000 LWM investment credit that was
    disallowed in error.
    As an aside, we note that plaintiffs also challenge the government’s
    defense of substantial variance on the basis of waiver. Specifically, plaintiffs
    contend that the government’s defense was waived because it was not timely
    raised. Plaintiffs note that the government did not state any affirmative
    defenses in its answer and waited to raise the defense of variance until the
    third round of briefing regarding the cross-motions for summary judgement.
    14
    Plaintiffs used the same language in both their administrative claim and in
    the original complaints.
    15
    In the amended complaint of the lead case, plaintiffs explicitly state their
    claim to the $10,000 credit. Pls.’ Am. Compl. ¶¶ 9-13. The government did
    not raise the defense of variance in its answer to the amended complaint.
    28
    Waiver of the variance defense occurs when “the Commissioner
    through his agents dispensed with the formal requirements of a claim by
    investigating its merits.” Angelus Milling Co. v. Comm’r, 
    325 U.S. 293
    , 296
    (1945); see Computervision Corp. v. United States, 
    445 F.3d 1355
    , 1365 (Fed.
    Cir. 2006); see also Consolidated Coppermines Corp. v. United States, 
    296 F.2d 743
    (Ct. Cl. 1961). The rationale for the waiver exception to the doctrine
    of variance is that
    Treasury Regulations are calculated to avoid dilatory, careless,
    and wasteful fiscal administration barring incomplete or
    confusing claims. But Congress has given the Treasury this
    rule-making power for self-protection and not for self-
    imprisonment. If the Commissioner chooses not to stand on his
    own formal or detailed requirements, it would be making empty
    abstraction, and not a practical safeguard, of a regulation to
    allow the Commissioner to invoke technical objections after he
    has investigated the merits of a claim and taken action upon it.
    Even tax administration does not as a matter of principle
    preclude considerations of fairness.
    Angelus Milling 
    Co., 325 U.S. at 297
    (citations omitted).
    Plaintiffs are correct that the government did not raise any affirmative
    defenses in its original answer or its April 11, 2014 answer to plaintiffs’
    amended complaint. The government’s first mention of variance is in a
    footnote of its reply brief, which was filed on February 11, 2015. When asked
    by the court about this footnote during the first oral argument, defendant
    admitted that it was not actively pursuing the defense but simply had questions
    regarding variance. Tr. 45 (March 18, 2015). Defendant did not begin
    actively pursuing the defense of variance until its June 16, 2015 supplemental
    brief. Defendant had multiple opportunities to timely raise the issue of
    variance and, instead of pursuing this defense, failed to include it in its answer
    and denied its potential application to this case during the March 18, 2015 oral
    argument. While our holding above removes the necessity of ruling on the
    issue of waiver, we note that the government’s litigation strategy demonstrated
    its intent to waive the defense of substantial variance.
    29
    CONCLUSION
    Plaintiffs are entitled to a refund of taxes, interest, and penalties
    attributable to their pre-1983 carryover credits of $73,384 and the $10,000
    LWM investment credit. The taxpayers, however, are not entitled to a refund
    for the sums associated with their suspended loss claims. Thus, plaintiffs’
    motion for summary judgment is granted in part and denied in part.
    Defendant’s cross-motion is likewise granted in part and denied in part. The
    parties are directed to attempt to stipulate the amount of judgment in plaintiffs’
    favor and report the result to the court in a joint status report on or before
    December 11, 2015.
    s/ Eric G. Bruggink
    Eric G. Bruggink
    Judge
    30