I have what I think is the same problem, and I think I've solved it by
installing the mainline kernel:

System:
AMD X2 3800+, 1GB RAM,
/dev/sda 1 TB
/dev/sdb 500 GB
/dev/sdc 500 GB

Symptoms:
Very slow reads (in particular) and writes to/from /dev/sda
hdparm -Tt reported /dev/sda as buffered reads at 50 - 60 MB/sec, however a cp 
from /dev/sda to /dev/sdb occured at about 6 MB/sec, and a cp to USB occured at 
1-2 MB/sec - during which the system was almost non-responsive - top showed 
iowait at about 60%. Paging in/out of RAM is glacial.
I also tried adding various params to fstab (noatime, etc) and changing the 
scheduler, to little effect.

Solution (please note, I'm running Ubuntu AMD64 with the nvidia driver blob!! - 
your mileage may vary):
As recommended by guiguy (thanks!), I downloaded the mainline kernel. I also 
needed nvidia drivers, so I followed the procedure here (post by Zeroth Eksaz  
on 2009-06-12):
https://bugs.launchpad.net/ubuntu/+source/nvidia-common/+bug/384639

In a nutshell, I went here 
http://archive.ubuntu.com/ubuntu/pool/restricted/n/nvidia-graphics-drivers-180/
and downloaded
nvidia-180-kernel-source_185.18.36-0ubuntu9_amd64.deb
nvidia-180-libvdpau-dev_185.18.36-0ubuntu9_amd64.deb
nvidia-glx-180-dev_185.18.36-0ubuntu9_amd64.deb
nvidia-glx-180_185.18.36-0ubuntu9_amd64.deb
and installed them all with 
sudo dpkg -i nvidia*185.18.36*

then I went here
http://kernel.ubuntu.com/~kernel-ppa/mainline/v2.6.32.2/
and downloaded
linux-headers-2.6.32-02063202-generic_2.6.32-02063202_amd64.deb 
linux-headers-2.6.32-02063202_2.6.32-02063202_all.deb
linux-image-2.6.32-02063202-generic_2.6.32-02063202_amd64.deb
linux-source-2.6.32_2.6.32-02063202_all.deb
and installed them with
sudo dpkg -i linux*2.6.32*

I watched this process via iotop, and had disk reads and writes
generally less than 1-2 Mb/sec, with iowaits around 60% and the system
almost non-responsive. Booting into the new kernel (with nvidia still
working), I can now cp from /dev/sda to /dev/sdb at about 40 MB/sec
(though I've yet to extensively test it - it feels a lot more
responsive)

Now, I realise I'm running a newer kernel to that from before, so it's not a 
like-for-like comparison, but I still think it's likely that guiguy's theory 
(about the problem being with an Ubuntu kernel patch) is likely to be correct. 
If people can suggest some tests for me to do that might help, I'll try and be 
of assistance, but this is the main PC in my house, and is needed!
I'm certainly going to be wary about applying future ubuntu kernel upgrades! 
(might try and stick with the mainline kernel - what a pain!)

Hope this is helpful, and Merry Christmas :-)

-- 
Slow SATA performance
https://bugs.launchpad.net/bugs/119730
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