The only thing I can think of, is you may not have entered the state distribution amount in box 16 of the 1099-R forms (even if empty on your paper/PDF 1099-R forms). You can't get a deduction for NY state retirement income not reported in box 16.
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@Opus 17 Other thoughts?
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*