I know exactly what you mean.  After using the Write Off Invoices under Accounting Tools, customer balances in the Customer Center show balances larger than what they actually are.  Now, even if I delete the Credit Memo that tool created, the Customer Center balances get even larger than they actually are.  I too don't know what to do to get the Customer Center balances inline with actual open invoice balances.

Has anyone found a solution to this problem?