Hi,
I have had similar problems. What you are actually wanting to do is refund the customer rather than just give them a credit note. The issue is that Express Accounts doesn't have a use credit note for refund feature which it really needs. One way around this problem would be to delete the customer's payment and then use the credit note to pay the invoice. A note could also be made on the credit note of when the original payment was made so that there was still a record.
I hope this is helpful.