In Keener, the Tax Court ultimately issued stipulated decisions in the partnership-level proceedings finding that the adjustments to partnership income and expense "were attributable to transactions 'which lacked economic substance,' as described in former I.R.C. § 6621(c)(3)(A)(v), 'so as to result in a substantial distortion of [partnership income and/or expense],' as described in I.R.C. § 6621(c)(3)(A)(iv)."

In Keener, the court found that the taxpayers' statute of limitations claim was "attributable to a partnership item" and therefore was barred by section 7422(h) from being litigated in a refund action.

In Keener, the court's reasoning was directed to the statute of limitations defense as a general matter and was not limited, as the appellants contend, to section 6229. Although the Keener court referred to section 6229 and did not mention section 6501, it is clear, given the interaction between sections 6501 and 6229, that the court's reference to section 6229 was merely a shorthand way of referring to the taxpayers' overall statute of limitations claim.

In Keener, the court rejected the taxpayers' argument that § 6621(c) interest should not have been assessed against them because the transactions for which that interest was imposed were not "tax motivated transactions," as required by § 6621(c).

In Keener and River City Ranches, the courts distinguished between the actual assessment of interest under Section 6621(c) by the IRS, which requires that the partner's tax underpayment was greater than $1,000, and the factual determination of whether a partnership was engaged in sham transactions.

In Keener, the court concluded that Section 6621(c) interest is an affected item with a partnership-item component and a nonpartnership-item component.