It should still be excluded on your NY return even if box 2a shows the amount as taxable. What button did you select on the "Where is This Distribution From?" screen?
Does the amount appear on line 26 of the IT201 (subtractions)? If it doesn't click on line 26 to highlight it and then click on the magnifying glass icon. This will take you to the Pensions/Annuities/IRAs Worksheet. Make sure the "Qualifies for government exclusion" box is marked at the top of the form.
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