Go back and edit that 1099-R in the Federal section.
On one of the pages as you continue after the main form page, you will see the page below, where you need to select the proper pension source for that 1099-R.
The NY distribution amount is not a zero...(as noted in the picture.) The NY pension source selection uses that Distribution value to subtract it from NY income...provided the pension source is fully not taxable.
That's OK. Just set it, work your way out to the table of 1099-R forms, and don't go back.
Several states have multiple selections that all point to the exact same exemption code in the underlying State tax forms. There is nothing in the actual submission that specifically says Military, or NYS Teacher's 1099-R....thus a military pension gets the same exempt-from-tax status as NYS Teachers....but the US Govt/Military selection is at the top of the list.
Yeah...would be great if the software would "keep" that selection and stop driving people nuts.