What I-Worm type viruses do is infect files outside the usual system locations like files you save in folders you have created. Other types of malwares can simply be copied onto the root of the drive and then create new startups every time the system is started or restarted even after cleaning the system registry.
Another thing to look at is temps,, cpu and others. One option to see if something is still infecting the system is running a few other types of removers.
Ewido works well catching things AdAware SE doesn't and likewise AdAware goes after what Ewido misses. Webroot Spy Sweeoer, Spybot S+D, and several others can be tried out. But one way to determine if anything left is causing the problems being seen and not hardware related is the "install to repair" option where Windows is restored long enough for a total sweep of the drive while in safe mode.
http://www.michaelstevenstech.com/XPrepairinstall.htm