Quickbooks Desktop have now added a field "Representative Identifier (RAC)" to their EFile T4 page.  Type in here your RepID and then Submit.  The xml file can then be uploaded through CRA represent a client to submit T4 Return.  I have successfully done this now with three of my clients with no error messages from CRA.  Would have been nice if QBD actually released an update to its users letting us know, I found out by accident whilst trying to find a work around for the problem today!