Payments have been recorded as entries in an AP Payment Batch, but they do not show up in the Bank Reconciliation screen.
When a Payment Code having the Payment Type 'Cash' (note: payment types are specified in AP Setup / Payment Codes) is entered into the Payment Code field on the header of the payment entry screen, an additional field called 'Cash Account' is displayed.
When the Cash Account field is populated with a GL account, this field overrides the Bank code (in this screen shot - CCB), skips the bank rec module, and the entry goes directly into the GL, even if the GL account code specified is for the actual bank account. In order to enter a cash transaction and have it appear in the bank reconciliation, leave the Cash Account field blank. Then the entry will go to the Bank code specified, and into the bank rec module.
The Cash Account field is most commonly used for recording Petty Cash purchases, where the Petty Cash account is not setup in Bank Services.
To correct the bank rec and allow for the missing transactions, do a bank entry for the amount of the payment, as a withdrawal, and code it to the bank gl account. This will result in the entry showing up in the bank rec (to be reconciled) and there will be no net change in the GL, since the entry created will debit and credit the bank account, avoiding duplication, since the original entry from AP is already in the GL.