In the Fed section, after you entered the 1099-R make sure to complete all the following screens and indicate which kind of retirement plan it is so when you get to the state it is handled correctly.
Look at the state return ... NY uses the total federal income to compute the state taxes and then it is prorated to the NY taxable amount ... so when you entered the 1099-R you may have seen the state refund go down and this is correct.