Look at your W-2 again.
Only box 2 $$ count against your "income" taxes.
Boxes 4 and 6 are for SS and Medicare....those are not part of your income tax calculations.
IF your box 2 $$ are wrong on your software W-2 form, then edit that form in the software and make sur each box is correct as compared to your paper W-2
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*