As I have been digging into the app store problems it is AMAZING how fragile it is. One simple permission setting will break it.
I think I may need to put an update out asap that disables the reg permissions repair on Win 8 till I can find what keys it is complaining about.
The funny thing is even when I add everyone full rights to every key (It is something under hkey local machine from my tests) it doesn't matter. It seems that Microsoft sees any permissions change at all to certain keys it wont install apps. It must be some sort of DRM they are using. Problem is NO ONE knows which keys. Using process mon from sysinternals the app store hits over 10,000 reg keys!!!
So it truly isnt a permissions denied error, it is more a "oh someone change a permissions, they must be trying to install apps they didn't buy" type thing, that or bad programming on their part.
Shane