We constantly have to get out of the reconciliation page to go to the general ledger to see if something has already been recorded as a journal entry. Journal entries should show up on the ledger side so that they can be matched with transactions on the bank ledger side. Regular checks, wires, transfers, and automatic debits all show up. So should journal entries.
Which types of transactions are you recording as journal entries instead of using a deposit for incoming funds and a payment for outgoing funds?