Alot of the newer trojans and spyware will run two processes. The two processes will check on each other and even if you manage to end one, the other will start it back up. Also if you edit the registry/msconfig, the program will continually check to see if its "run" line is in the registry. Best way to remove anything is to boot up into safemode. If for some reason safe mode doesn't work, then I like to edit the registry manually or using hijack this, then right after I make the changes, I pull the plug on the system then reboot. This way the programs have no hope of undoing my work.