Well thanks for clearing it up for me.  In the 'old days' I had to set an RC code up myself in SimpleStart and it never applied the totals correctly to the boxes then.  However, at some point it seemed to do it correctly so I have stuck with it until HMRC started flagging up the anomaly.  (must admit I had stopped double checking as I trusted my accounting system was doing it right)

Will use ECS going forward - thank you!