Sounds like the trojan infected some system files and when your AV got rid of it it deleted the files or it altered the registry to point to itself instead of the normal things. Look up the trojan on the internet and see if there's a fix for the registry or the files it infected. I know Sircam does this, a friend of mine got it on their computer and when I removed it they couldn't run any programs, I had to find what section of the registry it altered and change it back.