If you are having this discrepancy, here are the things that you should check:

  1. Are all Journals posted?
  1. Run a Detailed GL report for the AP account.  Were there any other postings other than Vouchers or    Checks to the AP account?
  1. Run a detailed Payable Report to see if any postings of  Vouchers went to a different AP account than the  normal AP account.
  1. Check the AP Setup to see if you are using the AP account for the Discount Account.
  1. Make sure you are running a current Aging report and checking against a current GL figure.

These are the leading causes of apparent discrepancies.