Let's get this straightened out so you can match your 941 form with your Payroll Summary report.
QuickBooks Desktop set’s its own calculation for 941 Forms. The calculated amounts in the form are based on the amount of wage base multiplied by the rate. This is to make sure the form will have the correct amounts. For lines 5a, 5b, 5c, and 5d.
I'm glad you've reached out to us. Let me help provide some insights on how to balance the 941 to W-2 Form.
In order to correct any discrepancies and balance both of your 941 and W-2 Form, you'll need to process liability adjustment. You can check this article for the detailed steps: Adjust payroll liabilities.
To further assists you with the steps and to check the setup of your S Corporation payroll item, I recommend calling our QuickBooks Desktop Support Team. They additional tools to take a look at your account and do a remote session.