>>the stipulated facts in the ruling [emphasis added] <<
Added emphasis notwithstanding, you are assuming too much. The Court goes on to say, "for reasons the record does not show,[3] the return that VTS prepared did not include the $3.4 million." The footnote spells it out even more clearly. "In their briefs petitioners seem to imply that the omission was the result of mistake or oversight by the C.P.A. who prepared the return. However, the stipulation does not state the reason for the omission, and because petitioners chose to submit the case under Rule 122, they did not call the C.P.A. as a witness. Thus, we do not know why the $3.4 million was omitted."
That judge is no dummy. He saw that the taxpayers' lawyer took pains to avoid actually saying the CPA screwed up and didn't let the CPA tell his obviously relevant side of the story. And that WAS the issue. The taxpayers' position was that the penalty should be abated for reasonable cause in that they had relied on professional advice. But over and over again the judge says things like, "preparer's unexplained omission." He didn't believe them, and neither do I.