I recently had to deal with something like this and found out that the State returns often use total wages, then they have an adjustment or credit later on in the return for wages earned outside the state or while non-resident.  I had to work with the help desk to get it to work correctly - there were certain fields that had to have a value to trigger it to do what I needed it to do.

I assume you have done the non-resident state entries?  

I would preview the non resident form and try to trace it to the state return.