Weird registry issue after Windows 7 repair install

I did a repair install of Windows 7 Professional x64 to solve a problem sfc /scannow found, but couldn't fix even in safe mode.
The repair install solved that problem. It however created a new weird problem in the registry. Now HKEY_CURRENT_USER and HKEY_USERS>S-1-5-21 have thefollowing keys that weren't there before the repair install. I ran Disk cleanup and got rid of all the unnecessary files after the repair install.
I also ran Ccleaners registry cleaner after installing all Windows updates and rebooting computer after all Windows update installs.
Here are screenshots of how the to categories keys currently look.
Security Essentials and Malwarebytes haven't found any infections in regular mode or safe mode.
I'm completely stumped on this one. Especially as the computer is operating normally. I had one BSOD that was do to my mouse driver not installing the repair install. That problem was taken care of by TorrentG on Saturday afternoon.

Your system seems to be corrupted. With all the issues you are having I recommend a complete reinstall. And that way you won't have any pieces/remnants of products TorrentG told you to remove and your registry is fresh.

Thats What I figured. Just wanted to see if there was a way to fix it without a clean install. Thanks