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For crying out loud. this is driving me insane ... by Klaranth2006-12-13 16:31:37
  Some background process doing CPU-blocking I/O? by Narc 2006-12-13 16:51:35
Or something CPU-blocking, anyway. I've had this type of problem while running WhatPulse (but I still stubbornly run it - I just kill it when I play something that requires fast response times), which intercepts keyboard/mouse events and probably sometimes blocks something somewhere along the line.

So my suggestion is try killing every non-essential process on the box and see if it keeps happening. If not, try starting background processes until it starts happening again.

Possible blockers include on-access anti-virus scanners, on-access anti-spyware scanners, and pretty much anything else that performs useful functions in the background.
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