Would you mind running a small experiment?
Install Athcool - it's a small program designed to make the CPU run cooler and use less electricity... Google for it...

apt-get install athcool

And the run it with -

athcool on

And see what happens... It ran fine on my test box a little Shuttle XPC the CPU temps came down about 7'C, but on my new production box, it just seems to hang the whole machine... not nice. So I'm wondering if it's the chipset it doesn't like or just something I've done...

Thanks in advance,
Lee

Search the forums for athcool it's a known problem, the stunt that it uses isn't kosher for all motherboardsand BIOSes.