The tax amount on a W-2 are the sum of each tax item's amounts. Same for the related wages for most taxes, except Box 1 which is special. The amounts and wages are never pro-rated based on earnings items.
Box 1, if that is what you are saying looks wrong, is result of the sum of various payroll item amounts. Items are includes based on their tax tracking types. All compensation items, for example, are included, as are tax-sheltered deductions like a 401k, and also any additions and deductions that have an applicable tax tracking type.
You can see which payroll items are included in Box 1, as well as each of their amounts and the total, by running the Excel-based "Annual W2/W3" report. Run it from the QuickBooks menu by selecting Employees | Payroll Tax Forms & W-2s | Tax form Worksheets in Excel.
