The NYS Pension/ Annuity Exclusion amount only affects your NY adjusted gross income by making it lower which would consequently make your taxable income lower, making your total taxes lower which should in effect make your refund "higher", not 0.
Make sure you checked off in the federal input that this was "Other Pensions of NYS and Local Govt's
the NY distribution amount would have flown through from your 1099R input entered here
and here
Eventually, it will lead you to this screen
and will flow through to forms like this IT 201, pg. 3
It worked well for me so I hope it does for you the same.