I filed an amended 1040, my New York State form figures changed but when I printed the return it did not say amended as the 1040 did, why?

I had not rec'd my New York refund, when I inquired they requested copies of my 1099R's, when I forwarded them I also sent a copy of the tax return with the updated amount.  I rec'd my refund from the original return but I am now informed I owe them the money, why?