Thanks for sharing the details with me, @ablehome1.
I see the importance of having your taxes accurate. Rest assured I’m here to help and guide you out of your confusion.
I have some steps that we can perform to get around this issue. I recommend running the Verify and Rebuild utility tool. This tool easily identifies uncommon issues within your company file and fixes them right away. To start, you can follow these steps below:
Welcome to the Community. I can provide some clarification about the updates in QuickBooks Desktop.
The Automatic Update option is designed to ensure the software is up-to-date and has the latest features and fixes. However, the payroll updates aren't part of it because its only applicable for users with an active payroll subscription.
Tax table updates help ensure the program follows all current laws that affect payroll calculations. We recommend keeping QuickBooks and tax table updated at all times to avoid any unexpected behavior.
If your recent payroll is already provided to your employees, the adjustments should reflect to the next pay date. It should include the missing taxes.
I can see how beneficial having a button for auto-update and being warned to download the recent tax table during payroll. We always update the features in QuickBooks, and this preference might be added in the future.
As we assess this, I suggest you visit our New Features section (click the Help tab at the top, then select New Features) to stay updated with all the changes that are being made.
Also, for additional reference, you can use the following articles to learn how to fix paychecks with taxes not calculating, as well as incorrect wages and taxes in QuickBooks: