After reading social.technet.microsoft.com/Forums/en-US/720f6515-47fc-4805-8ccb-dc144cb72078/action?threadDisplayName=gpo-backups-import-merge-export-problems I think I've identified that some of the differences come from the Not Defined/Not Configured
settings not being backed up in the GPO Backup. I can live with that.
The other issues are attributed to flaws within SCM 3 regarding GPO Imports...hopefully they'll be sorted out by the team soon.