When viewed in the Reconcile window, the deposits do not display the check numbers.
Althouh there is a column for check numbers in the Make Deposits window, the check numbers will not display in the Bank Reconciliation screen because the reconciliation window identifies the deposit and not the transactions within it.
Note: This workaround is only applicable to single item deposits.
When entering in deposits, you can enter the check number in the memo field in place of the word 'Deposit'.
In the Reconcile screen, you need to add Memo as one of the columns to display so you can view the check numbers.