I decided in the end to revert to a previous backup and take a look more closely at what the product did. I tried doing things more slowly and I think I discovered what may have been happening there was a directory that should not have been where it was, that I think was adding to the confusion. Now without even running the windows repair tool I have SFC and DISM both working as they should be and the corruption I had, has been repaired.
That said all the re-parse points you create are just not present on the current WIN10 builds so I wonder why you create them in the first place. They may have been there on older Windows versions but are not required now. Should Windows repair be more observant of which windows version it is attempting to repair? It makes me wonder what would have happened if I had gone onto look at the registry bits and what would have perhaps been done that was not required or at worst incorrect.
