matching transactions from the bank feed will not fix it (matching from  a bank feed just keeps the transaction from being double posted).  If you look in the transaction journal for the refund receipt, you will see that it credits the undeposited funds account and debits an income account. It shows up on the customers account but it is not actually posted to Accounts Receivable hence there is nothing to apply to the customers credit balance.  I do not understand why they don't give you the option to post to A/R instead of an income account but that is the case.  The simplest fix is to:

1) create another Customer invoice (I use the same invoice # as the refund receipt with an appendage to distinguish yet connect the entries.) and use the same product/service as the refund receipt.  The debit on the refund receipt and the credit on the invoice will cancel each other out so there will be no affect on income (which there shouldn't be with an overpayment) but allows for a debit to A/R

2) If in same month, just re-open the original payment and apply the overpayment to the invoice and you're done!  (This is what I did in the sample copy & pasted below.)

3) If not in same month, "receive payment" for $0 on the new invoice you just created and apply the overpayment 

It's a pain but the simplest work around I have found.  I tried calling support to see if there was any other work around but they knew less than I did.