Any antivirus you run that tells you that you have registry problems is probably a bad antivirus unless it's actually locating a virus' entry.
Registry cleaners don't do anything.
I'm thinking you may have a TDSS rootkit which can be cleaned but there is no guarantee your computer will ever be safe again unless you format it. Many antivirus' will not pick up a TDSS rootkit.
http://support.kaspersky.com/faq/?qid=208283363
Run that first.
Then run GMER.
http://www.gmer.net/
I would then run Dr Web Cure It.
http://www.freedrweb.com/cureit/?lng=en
After all that, and you still think it is a background process, just press CTRL-ALT-DEL and see which process is using up the most CPU cycles or memory.
Those are just my "hit the broadside of the barn" suggestions based on the little information you have.