Comment 147 for bug 119730

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 :-)