TimeTrex Time and Attendance

One of my W2's this year has a different total for Medicare Wages (box 5), than the totals in boxes 1 & 3. There were bonuses paid from the commissions pay stub account, but it's set up as an earning account. Also, the total bonus amount is not the same as the difference between Medicare wages and the other wage totals. Any idea what I'm looking for here?

On the W2 report, under the "Form Setup" tab, you see and change which pay stub accounts get allocated to each box on the W2.