This is a much easier task given a tool like GridView.

Find out when they got out of synch if you can.

Make sure all the transactions in the control account came from AP by filtering them for the source code AP. In Ledger you can create a custom Source Journal to list just those transactions that don't have AP as the source. You can also use the transaction drill down in the financial reporter to get the details into Excel (or the ExcelDirect button on the transaction inquiry in Ledger V9.0B).

This might quickly and easily point to the problem.