Hmmm, msconfig not working on its own keys? Sounds a little odd, but then an OS that needs a registry is a little odd.
I'm not sure about residual damage but if you got all copies of the executable and the system works, I'd say you're fine. I still highly recommend COMODO, it really is the ultimate shield on a Windows PC. I have not had a virus for so long, I don't even remember the feeling.
"Oh nonZero, let me tell you, I love you." -- Dark Java Dude 64, Vice-Kapitan of nASA(nonZero's Awesomeness-Spreading Association)