Welcome to the Community, @GreenRoomGraphics. I appreciate you for sharing every detail of your concern. I can help you handle your entries so payments will match correctly.
QuickBooks will record the payment depending on the invoices selected under the Customer Payment window. Since the system tries to reassign the payments back to the incorrect transactions, you may disable the automatic payments feature as this may affect the issue.
Here's how:
- Open your QuickBooks Desktop (QBDT) file.
- Go to the Edit menu, then click on Preferences.
- Tap on Payments on the left panel, then Company Preferences.
- Untick the box beside Automatically apply payments.
- Hit OK to save the changes.
Once done, observe the payments once your client pays their invoices. If you're getting the same result for skipped invoices, I recommend running the Verify Rebuild Tool to fix possible data issues within your company file that affects the issue.
You can also check this article for more details on how to use the QuickBooks Tool Hub to fix problems and errors you've encountered in QBDT: Fix common problems and errors with the QuickBooks Desktop Tool Hub.
The Community page is available 24/7 for assistance. If you have follow-up questions about your invoices and payments, let me know by adding a comment below. I'm more than happy to help. Keep safe!
