Why Reconcile Clearing Accounts Automatically did not work?

1. Reconcile Clearing Accounts Automatically was initially run but did not reconcile some transactions automatically even if the JE lines have the same reference and the Debit and Credit amounts are the same.
2. The Reconcile Clearing Accounts Automatically was re-run and the previously unreconciled transactions with the same reference and Debit & Credit amounts are now reconciled.

What can be the the possible explanation for this?

Thanks