Sorry to hear your troubles. I agree with Julien, sounds like electronics. We've had this same kind of issue as well on our XP, and, to make a long story short, it was the ion source control board that was faulty. I would suggest that you try and scan the plates to be sure the problem does not reside in the ISCB. It's easy to tell if you have a bad plate-the scan won't be a nice curve, which means that maybe an op amp is bad. I also suggest that you scan either the box or trap current, to see if the cathode can be maintained at a constant current.
Hope this helps,