Hi shlackinfrackin,
Hmm, that's odd. I guess it must be to do with the vast amounts of missing registry keys. As these are Windows Update registry keys, the repair install must be getting confused about what's installed and what's not. I hate to say it, but I think the only thing left now is to go for a clean install:
Clean Install Windows 7
Sorry I couldn't have been of more help, but there is really no other way.
Tom