Why do Customer Payment & use of Credit(other unapplied Payment) not recalculating Commission?

We have several unapplied payments for a Customer and they were identified as overpayments. We sent the Customer the amount and asked them to enter it as a credit on their side so the next time they pay us they will use that amount. So we call them credit memo's to the Customer but they are really just unapplied Payments. Once the Customer pays for a new invoice they will pay less that previous amount. We create one Payment record from the Customer, and enter the amount received and post to the invoice and then select