OK looks like I got it fixed.
When to took the default permissions from Windows 8 it was from a fresh install, nothing installed or added and every single windows update done. Well I had forgot to install the key for the media center.
So I updated the fresh install with the media center key, then ran all the latest updates from this last patch tues day plus any that might get installed with media center being back on. I then export out the default permissions again for a up to date list.
On my other test Windows 8.1 in vmware, I use it to purposely break things and then fix them. So I installed media center, ran the registry permissions and media center crashes just like you said.
I then copied over the updated default permissions, ran the registry repair again (Without restoring the registry from the last scan) and rebooted, A bang, Media Center is working
So v2.8.1 will be released on Monday, July 14th 2014. Till then here are the updated files, if you dont mind testing and verifing for me
Take these 3 files I posted and replace the ones in the folder with the program under "\files\permissions\8"
Once you replace those 3 with these go ahead and try the repair again and let me know the outcome
Shane