I know this is a general answer, but...have you tried running chkdsk on your system since you freed it of malware?
XP Chkdsk, Using the Graphical Version (My Computer) - http://www.updatexp.com/windows-xp-chkdsk.html
One of the problems with malware (IMO) is that we users don't really know the extent of damage which may have been done to other files by the invasion.
Running chkdsk and defragging would be my first steps in trying to make sure that the system is working as it should.
After those steps, I would use Event Viewer to see what known troublesome items have caught the attention of the O/S. These items will appear as errors on the Application or Security tabs. If any time correlation can be made between the errors in EV and the errors you get onscreen, I think we might have an obvious winner
What is the Event Viewer, and Should I Care - Ask Leo! - http://ask-leo.com/what_is_the_event_viewe...uld_i_care.html