I used to be affected quite badly by this problem, through all of
Intrepid and into Jaunty.  My system's no longer affected.

What eventually appeared to resolve the problem for me was a combination
of newer kernels (somewhere in Jaunty's updates, sorry I don't have a
version to reference) and a motherboard BIOS update - everything related
to SATA disk access got noticeably more stable with newer BIOSes.
Jaunty became quite usable, and I haven't had any problems in Karmic.

So to anyone currently still experiencing this problem:  see if there is
a BIOS update available for your motherboard, and ensure you're running
the latest kernel in Jaunty/Karmic.  If you're still pre-Jaunty,
consider upgrading.

Just my $0.02.

-- 
Heavy Disk I/O harms desktop responsiveness
https://bugs.launchpad.net/bugs/131094
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