@itonewbie , were i to rewrite your reply, it would sound something like, ‘NY and NYC generally conforms with the IRC on a rolling basis, but  occasionally (well, maybe more than occasionally) makes a hard left turn and completely departs from conventional tax theory.  🙂... there wasn’t enough info to understand exactly what the OP was referring to... just hope that he and the software has got it right. 

...a friend of ours sent me an email once complaining that NYC did not recognize an SCorp and treats it as a C. The result was that the NYC business owner/resident ended up paying a double tax on the same income.... the only possible response was ‘yup’.