I've also had this problem with Turbotax when entering in the NYC TRS distribution. I believe you have to enter the 1099R taxable distribution into the state section (box 16) when completing the federal income section. (I also had to enter the payer's ID number as well.) You will then have to answer the following questions posed by Turbotax. This should then correctly post the distribution on the correct lines on NYS forms and subtract the full distribution amount.
I hope this helps.
Frustrated user.
