adamf83 I ran into permission issues in the past because of my sysvol (the one and the same hidden system file) not having the default and necessary permissions. I'm unsure as to how it got that way, but I checked the sysvol file on every partition that my Exchange servers had to confirm. After setting the correct (default) permissions, I was able to rerun the Exchange set up fully with no further errors about unauthorized access.
It was a couple years ago when this happened so I don't really remember the extent, but I think the sysvol was missing SYSTEM - Full Access. May need to make sure the local server group "Administrators" has full access too, but I'd only do that as a secondary step to the SYSTEM ACE.