Maybe try System restore and then do your system changes one at a time so you can find the culprit? I assume that you did complete scans for viruses and adware/spyware BEFORE you did all this?
I am on XP-SP2 Home. Every two minutes exactly my active window goes inactive - very irritating! This occurred soon after (and possibly simultaneously with) upgrading to SP2. Unfortunately I made a lot of other system changes at the same time. I've tried deleting tasks, and there is a point that the problem goes away, but it isn't obvious what task is causing it. I've also reviewed logs but saw nothing that occurs simultaneously with the problem. Any help is appreciated.