Let's check your bank register and make sure the transactions have not been reconciled. Here's how:
Click on the Accounting tab.
Click on Chart of Accounts.
Look for the bank account, and click on Account history.
Click the Filter icon and select a date range of the period you wanted to reconcile.
Check if the transactions does not show an R.
If it showed an R in the check column, this means the transactions has been reconciled. Reconciled transactions will not show in the reconciliation page.
If the transactions shows in the bank register, kindly check the transaction date and make sure it is with in the reconciliation period you are trying to reconcile. I would also recommend cross matching the transaction with your bank statement making sure they're the same.