For systems getting long in the tooth, (even if just a little) I would try Debian and maybe SliTaz. Or for a 'buntu, I would try Kubuntu 11.10 Oneiric Ocelot or Ubuntu Lucid Lynx.
It's a real bad Fdisk bug. It always worked fine with another program to partition the HDD. I noticed this problem (or similar) back in 2002 when I got a Maxtor 4D080H4 80 GB.
I gotten word that a throttling processor can cause the OS to report high CPU usage percentage. (When it self-underclocks because of reaching close to 90 C) The heatsink may not even be all the way on the chip. (more common with the darn 775 push-pin heatsinks than with a 478) Or a lot of dust.