Create Accounting Issue - Reconciled Payments

We have a client where Cash Management was implemented the month after they originally went live.  Payments that were generated the first month in Production credited cash direclty.  Problem now is that some of these checks are starting to clear the bank but when we clear the payment in Cash Management the resulting creating accounting is failing for these transactions and I am assuming it's because the payment was originally credited to cash and never hit cash clearing.  Does anyone know how to resolve this issue since it is now causing us to not be able to close the Payables Period