Thanks for the reply.
1) Yes I filed non-res NY and res NJ forms
2) Yes my employer is only taking out NY taxes
When I looked more carefully into the underlying forms behind turbo tax, I traced it down to one thing but I still can't explain it. In the NY Forms, Part-year resident/nonresident allocation worksheet, it shows Column D as income from NY sources. For row 1 (Wages), it is showing a number that is lower than I expect. I then traced that number and found it in NY State Wages/Self-Employement Income Allocation worksheet. In that worksheet, it shows two W2s that I have but one of them is much lower wages that I expected. It does show 100% allocated to NY which is correct but the total number is wrong. I am unable to trace where Turbotax is getting that number as it is not shown anywhere in my actual W2s. When I look at the Wages for NJ, it has the correct numbers for the W2s and when I look at Federal, it too has the correct numbers. Since NY is using a lower number, it is then calculating lower tax resulting in a refund. This almost looks like a bug in the software.
Can you think of any reason why the NY Wages of a W2 would be much lower (about 30% lower) then the wages reported on the actual W2?
