The present subject matter relates to a method and system for increasing the throughput of mail processing machines by limiting the number of document processing system stops while effectively allowing errors to be reconciled during the continued operation of the system. More particularly, the present approach involves logging detected errors during an ongoing document processing run. The detected errors are analyzed for priority, and the operator is alerted to take corrective action during run time for specified errors. The reported errors may be reconciled prior to the completion of the document processing run.