There are a number of causes for control accounts not tying to their sub ledgers, including manual journal entries to the control account, transaction posting to incorrect accounts (should have posted to AP but posted to a different account), posting to incorrect periods, voided documents posted to the incorrect period, incorrect settings in the AP Trial Balance report definition, etc., etc. (Make sure you're running the 'Historical Aged Trial Balance' and in the 'Exclude' section, that all boxes are checked EXCEPT for 'Credit Balance'.)
The task of reconciling used to be a hunt and peck process before GP10. If you’re using GP10, then you have the 'Reconcile to GL' tool available to you. This tool analyzes the transactions in the sub ledger (in this case, the AP Trial Balance) and compares those transactions to transactions in the GL. Where a definite match occurs, such is indicated on the Excel file produced by the Reconcile tool. Where a match doesn't exist, or the match is not 100% definite, those are indicated in the Excel file also.
However, if you're on GP9 or a prior version, then the task is more difficult. You'll need to analyze your AP account transactions to determine the source of the transactions and whether they hit the correct period. SmartList is a great tool for analyzing individual transactions. Once you have the offending transactions isolated, fix what you can. Any remaining difference will likely require a journal entry to bring the AP account into balance with the APTB. Once you're reconciled, go to the AP Account Card and uncheck the 'Allow Account Entry' box to prevent manual journal entries posting to the account. In fact, you should do this for all your control accounts.
I also suggest to my clients to reconcile the account more frequently than monthly. Biweekly or even weekly may make sense, depending on the transaction volume in your environment. It's a lot easier to find these little glitches and correct them when the volume of data to pore over is less.
Oh, one other thing, check out The Closer from http://www.reporting-central.com/. This is a 'Reconcile to GL' tool on steroids that works with any version of GP. If I were responsible for a GP environment, this would definitely be in the toolbox.