Late charge calculation not considering onaccount or unapplied receipts

hi,

I have a customer with few overdue transactions. There is an on account and an unapplied receipt. Late charge generate program is not considering these receipts while calculating interest on overdue transaction.  As per the functionality late charge gets calculated on transactions only but how do i tackle issue relating to onaccount or unapplied receipt.

From customer perspective he has already paid some amount to us. Is there any workaround?