This is a stupid question but.....
After scan, are you going to "select" in the pull down menu and selecting "All" then "fix"? If you are, are they checked? Are you using "Raw List" under the "Results Format" tab?
Do you have administrative rights? I have had issues with other programs not working because of this and privileges.
I have Vista and Regsupreme Pro works fine (not that no one else should have a problem).