Now I'm really confused!

Normally, transactions flow from BankRec to Ledger, so I'm not sure what process you are following. When BankRec is installed, normally it takes over all entries to the Bank accounts, and you should not be doing any entries directly in Ledger to those accounts (like the AR and AP control accounts should not be touched in Ledger).

Since it doesn't sound like you have BankRec integrated with the general ledger in the regular way, I'm not sure what assistance we'll be able to provide through the Forum.