After you file

The tax withholding is not calculated at all. It is simply the total of all W-2 box 2 amounts that you enter and is reported on the 1040 line 25a. It 25a matches your W-2's then it is correct, so exactally what does the IRS think is wrong? Did an employer fail to report the withholding to the IRS?

No. Turbotax didn't use the paper W-2s that I received in the mail. They used W-2s that they downloaded from somewhere. It's clear that they had the correct information, because they calculated the correct amount. The problem is not in the W-2, it's in the way that Turbotax presented them on my return. They simply left out box 2 through 7.