I appreciate you promptly reporting this to us, Ron. I have a way to fix the issues you're having with applying your vendor credit to your Invoice.
In addition to marking the bill as paid via the Pay Bills function, you can utilize either the Expense or Check features to settle any open bills.
Here's how to close your open bills using the Expense or Check options:
Click on the +New button.
Choose either Expense or Check.
Select the appropriate vendor. A sidebar will appear displaying a list of bills and any vendor credits available for that vendor.
Click the Add button next to the bill you wish to pay. You will see that the transaction has now turned into a Bill Payment on the Check or Expense page.
Scroll down to view any available vendor credits and check them as needed.
When finished, click Save and Close to finalize the process.
In the report, you can use the Bills and Applied Payments or the Transaction List by Vendor to verify.
Here's how:
Go to Reports.
Search it there, either Bills and Applied Payments or the Transaction List by Vendor.