Do you have a Suspense Account in your COA and linked on the GL Tab of the Billing Program Level Set-up? I would double-check the set-up in both areas. When the overpayment is entered it should Debit Checks to be Deposited and Credit Suspense. The Suspense Account is a temporary holding account for transactions until they can be properly classified. You may want to consult with your accountant for more information.