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How To Assign Payments Received Properly In GnuCash?
When I receive a check from a customer whom I previously sent an invoice, I go to the customer report for that customer, click on the link "Invoice" for that invoice, then click on the Pay Invoice button (very far right side). I then do a customer report and see that there is no balance (meaning all the invoices have been paid). I don't process invoices using the same method you do.  Instead I go to Business -> Customer -> Process Payment.  From there I can select the applicable customer, and a list of unpaid invoices will come up.  I've never experienced the issue you've described. On a related topic: are you posting your invoices?  From experience that has caused issues for me; when you post the invoice it should show up in your Accounts Receivable (or whichever account you've designated), and after you process the payment the A/R should go down accordingly.  When posting your invoice, you specify which account it gets posted to:  So that account should show a balance once you have posted it:  Then, when a client pays you, your cash will go up, and A/R will go down.