Are you running the program in Aggressive mode?
The new RegSupreme Pro can also detect errors in encrypted system registry entries, the old version couldn't (nor can most other registry cleaners), this is why the new version shows that many more errors.
Most of these errors are, I assume, UserAssist entries. They are safe to remove, however, some MRU features of Windows will be reseted if you do so. One of such feature is the Personalized Start Menu of XP, clearing all UserAssist entries will clear it, but you can avoid the problem by not using the Personalized menus in XP.
Only the Aggressive mode clears all of these entries, so running the Normal mode should always be safe.