resurfacing Customer Credit Card Payments

I am using Quick books merchant services.  I keep having issues where a customer has paid by credit card, it has been deposited, and my checking account has been reconciled to a zero balance.  Then the payment shows up months later either in the merchant services deposits as needing to be deposited or another just showed up in my checking account reconciliation screen.  So frustrating because I don't know how to get rid of these without screwing up my customer balances (or my company balances).

Am I the only one with this issue?

Thanks!