Andy,
   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,
Ross