I can help you isolate the issue you're experiencing with your tx withholdings, flyingplow.
Make sure you are on the latest version of QuickBooks Desktop and payroll tax tables so the system can calculate your taxes correctly. Further, the employees' setup is correct and updates to their payroll information within a quarter or year can also cause discrepancies with how the system posts their withholdings.
You can try setting up the employees' info on a sample file with payroll and select the correct filing status. If it works, you can open your company file and perform the Verify and Rebuild Data Utility process. However, if the issue persists, you can run the QuickBooks Desktop Tool Hub.
Feel free to visit these links for more details on how taxes are calculated in QuickBooks Desktop:
Let me know if there's anything else that you need help with. Take care!
