We have one employee with long term calculation issues when it comes to Payroll. In early 2018, we discovered it was taking his Oregon withholding and doubling it, even though it was setup just once in his Payroll record. I remedied this by (if memory serves me correctly), having to remove his withholding info, save his record, then re-enter all that info.
We run reports and reconcile monthly, and also quarterly. What I didn't know until running his W2 for 2018, is that for payroll checks ran January -May of 2018, it took his Wage Base for each check and doubled it. This is not visible in his payroll history nor in any reports we routinely use. I found this by running the Payroll Summary report for 2018 and drilling down into the transaction data.
So, for his 2018 W2, his box 16 is $21,810.82 higher than box 1. This is the sum of the duplicate Wage base for the first 9 payroll checks of 2018.
I don't know what's causing this to just one employee out of 50, nor how to remedy it.
I appreciate you for reaching back to us and letting us know about the result here in the Community.
I'm glad to know that the Verify/Rebuild data feature helps you with the corrupted employee records in QuickBooks Desktop. By posting a response about what works for you, other users will be able to try the troubleshooting.
Please be sure to let me know if you need any assistance in the future. The Community is always available to help.