Please note/follow the steps below to further troubleshoot this issue:
1. Run a Trial Balance to make sure your division is in balance.
2. In Report Manager, Accounts Receivable, Invoices/Statements/Aging, Run the Aging by Customer report, and the Aging by Receivable report for all accounts. You can also run the Open Invoices by Receivable Report. All 3 reports should balance. The Aging by Receivable report, if run for all accounts, will show overpayments in the account designated for the overpayment contra account in your AR setup.
3. Whether your reports balance or not, after verifying you have run all reports on the same month-end date, it will be helpful to run an account detail report to find entries made to the AR accounts with a GL journal. You will most likely find there are entries made directly to the GL AR accounts. These entries should have gone through the AR module.
4. If this is the case, reverse the entries in GL and enter through the AR module. These entries will need to be reclassed.
5. There may be some cases where a user posted to an AR journal through the General Ledger. This can be spotted by looking at the journal and the srce column on the General Ledger transaction report. If there is an AR journal that does not have a source of ARS, it was probably posted directly into the General Ledger. It will then have a source of GLS.
6. If the discrepancy still cannot be found, you should run the same reports for different time frames to find when they were last in balance.