Could be a number of things causing the problem, but one thing to be aware of in the current landscape of malware is that stealth technology is becoming increasingly popular in malware design. I am not saying that you have stealthed malware, but it is a possibility as the symptoms match.
I highly recommend running all of your anti-malware scans in safe mode to reduce the number of processes that launch on startup. (Use 'safe mode with networking')
In addition I recommend sweeping with several different anti-malware applications.
Caveat emptor, a full sweep with the above software eats at least 8 hours of time. I usually budget two full days for malware removal if I am asked to save a heavily-infected system. More if it turns out to be something incredibly nasty, as the state of the art in anti-detection and anti-removal tricks advances faster than the good guys can keep up.
Rootkit Revealer and Hijack This will both have entries detected even on clean systems, and require some technical know-how to interpret usefully.
Finally, even with all the above software run, there is no guarantee that it will actually disinfect your system. Stealthing technology is a hydra, for every one method we learn to detect and nullify seven more rise to take its place.