The reports are including invoices that were coded to other payable accounts which you are not including when comparing to the General Ledger payable balance.

Use the Period End Report for AP Accts (AP Reports, GL Reconciliation, Period End Report for AP Accts) and click Ranges to select the payable accounts you are reconciling.

Tip: If you see an account in the Ranges that is not a normal Accounts Payable account, this means that one or more invoices had this account coded as the Accounts Payable account. If there are open balances on the erroneous account, these invoices will need to be corrected.