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CPU Usage doesn't add up
On checking Task Manager, it showed System Idle at 99% but CPU activity was at 44%. None of the processes shown in Task Manager were doing anything other than intermittently using the CPU for short periods of time at low percentage values which were reflected by a reduction in the System Idle Process. This 'invisible' process activity is almost constant and varies from around 20% CPU up 70+% CPU and is never accomapnied by a reduction in the System Idle process value. It is also accompanied by almost constant read write activity on the hard drive.
I ran Process Monitor and Process Master, neither of which showed anything hidden. I ran Disk Monitor which confirmaed the Hard Drive activity (mainly writes, but also some reads). I also ran Spybot, AVG Anti-Virus, AVG Anti-RootKit, Sophos Anti-RootKit and RootKit Revealer. Nothing showed up apart from some standard Spyware stuff in Spybot.
I've just about run out of ideas short of a complete system rebuild. Any help would be very much appreciated.