You can also view your Payroll Summary Report and compare the data on it with what you have on your incorrect last quarter's tax form.
If you already have the correct calculation, you can now re-run and submit the 941 forms.
If the issue persists, I’d recommend reaching out to our Payroll Support Team. A payroll specialist would be able to further check on your account on a secured environment and review how your payroll item is set up via a secured remote access session.
Go to Help.
Choose QuickBooks Desktop Help.
Click on the Contact us link.
Choose Search for something else.
Type in a keyword about your concern.
Click on the Start a Message button.
Feel free to visit us here in the Community if you have other questions about updating your payroll information. I'm always here to help.
Before you run the checkup, please back up you company file to keep a copy of the unchanged data. I usually advise this specially when a client will do changes on his company file which affects the past quarters.
Running the payroll checkup is one step to correct your payroll reports and W2s. This checkup will correct your wage base and determines your tax discrepancies after you changed the tax tracking of your HSA item. You can check the article about payroll checkup and see the Discrepancy column on the fourth screenshot. That's what I'm talking about.
The discrepancies will be used to correct your tax amounts. In other words, you will need to do a liability adjustment to correct your payroll data.