I actually fixed this problem. The scan was failing due to 3 missing directories. I found out these directories were removed by a tool I've used from nVIDIA Geforce 480 470 285 260 9800 275 295 GT GTX AMD ATI Radeon HD 5870 5850 5770 4890 X2 - Guru of 3D: PC Hardware Reviews
called the Driver
sweeper. It's normally very good for preparing your computer for updated video/sound drivers
to remove all traces of the old one.
This time, it went too far, it removed the 3 directories below and installing the new driver apparently doesn't bring them back.
These are related to my ATI 5970 graphics card.
What I did was break out an old hard drive, install Windows 7 on it and copy over the directories as it looks like they're the same, name and all.
After putting those 3 directories back, the scan completes and finds no issues.
Might have taken some time but overall less of a headache than reinstalling or trying to repair windows.