The Difference field in the Payment Reconciliation Journal lines when the line is Applied to a Bank Ledger Entry and Transaction Amount is less than the Applied Amount i.e. the Bank Account Ledger Amount.
When the Bank Statement line amount is less than the Bank Ledger Amount, the Bank ledger need to be closed based on the Bank statement hence need to post the difference to a G/L Account same as what happens when Statement line Amount is higher than Bank ledger Amounts. This is quite common in customers using NAV in retail practise otherwise the Bank Ledger will be open for ever which defeats the purpose of Bank reconciliations. This results in lot of unreconciled Balk ledgers which leads to AUDIT issues for complying best practise of bank reconciliations in accounting application.

The Bank Account Reconciliation age supports this scenario.