MBP with 10.6.8: CPU usage high, no responsible processes shown in Activity Monitor. What causes this?

After using my computer for some time, CPU usage climbs to about 90% (ca. 65% user / 26% system) and fans run at high speed, but there is no processes that seem to use CPU (other than Activity Monitor itself ~1%).
This has happened a few times recently. It happens when I've used my computer for some time, hours or a couple of days (I usually put my computer to sleep when not using it but rarely shut it down). I've tried to quit all running apps incl. Growl, Dropbox, and anything that could be responsible to this but with no results. Putting computer to sleep for a long time doesn't help, cpu usage will climb instantly after wake up. Restarting system is the only thing that helps.
Most of the time I use my laptop with external monitor, lid closed and connected to power supply. When experiencing this, opening the lid causes fans to slow down, but CPU usage remains high and battery drains quick.
Any ideas what might cause this?
My MBP is 15" model with Core 2 Duo 2,66 GHz (MacBookPro 5,3), OS X version is 10.6.8, all available updates are installed.

Perform a SMU reset.
https://support.apple.com/kb/HT3964
Remove the anti-virus, it's running a root level process all the time that's taking your CPU and it's not necessary as there are no Mac viruses, Apple has the trojan angle covered already.
Always on anti-virus on a Mac is always a source of problems, also is MacKeeper, uninstall that here if you have it.
http://applehelpwriter.com/2011/09/21/how-to-uninstall-mackeeper-malware/
If you need to clean the Windows filth off PC files, then use the free, run as you need, ClamXav.
http://www.clamxav.com/
It seems your machine is used in a corporate enviroment, thus likely a rule that anti-virus must be used, you can avoid high CPU usuage by using the ClamXav instead.

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