When the Bank Reconciliation window is opened, it is looking for Transactions that have the field TCLEAR = 5. When a Transaction has been marked as cleared, the TCLEAR = 6.
If for any reason a bank transaction is inserted and the TCLEAR is not set properly, the transaction will not show on the reconciliation list and it will be impossible to reconcile with the bank statement.
Go to Menus > Checks, then Checkbook > Transaction Inspector and select the transaction to unclear.
Alternate way of finding the transactions
You can find these transactions by going to Ledger > Reports > Audit Trail > Custom Search.
AUNUM = 1100 (or whatever your GL Bank Account is)
TCLEAR <= 5 (looks for invalide TCLEAR value)
TSOURCE <> CL (do not show closing transactions)
To fix, use the Programmers Transaction Window to Edit TCLEAR on the transaction to 5 (not cleared).