Hi annabel208
The bank feed transactions in the Bank transactions are brought into your file from your bank and matched to the MYOB transactions. If you allocate a bank feed transaction the software automatically records the applicable MYOB transaction. If there's an existing MYOB transaction you need to match this transaction with the bank feed transaction.
It's the MYOB transactions that are included in balances, reports and appear in the Reconcile accounts window. When you match/allocate a bank feed transaction in the Bank transaction window the MYOB transaction is automatically ticked in the Reconcile accounts window. If you manually tick a transaction in the Reconcile accounts window it won't appear to be matched in the Bank transactions window as the software sees it as already matched. As the Reconcile accounts window is only the MYOB transactions, the account will balance whether you match the bank feed (automatic tick) or manually tick the transaction.
If the account balances in the Reconcile accounts window it sounds like the pay transactions have been manually ticked. You would need to untick the pay transactions in Reconcile accounts, then go to Bank transactions and match the transactions.
If you've completed the bank reconciliation you would need to undo the bank rec, untick the pay transactions, match the transactions in Bank transactions and then re-do the bank rec.
If you continue to have trouble with this please send me screenshots by private message so that I can assist further.