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Thank you.  I'm going to have to ask to see my son's 1099-R, as I don't have access to it now.  Could it be that when asked about making non-deductible contributions to an IRA, he should have said "no"?  We said yes because of the other, regular IRA conversion that was done.

There was only one type of contribution- to an after tax 401k, and it was then moved in entirety to an outside roth IRA (but had appreciated slightly in the interim.  hence the $97 taxable amount).  My guess is that the 1099-R is correct, but that somehow, in answering questions, things got confused.