It seems i have found a solution which should work for at least Compal
notebooks. I found this based on information I found in one of the
duplicate bugs. It seems at least the ICH9 controllers have two modes of
operation. One is called IDE compatible or no-AHCI mode and is enabled
by default. This uses the ata-piix driver. If you manage to switch the
controller to AHCI mode it should use the ahci driver instead, which
does not seem to have any problems.

You can check what mode your controller is in using lspci. It will show
either IDE or AHCI depending on what mode is set. You can also check the
dmesg output for ata-piix or ahci.

Switching the controller to AHCI mode can be quite tricky. I was able to do it 
using a Dos program from Compal's site. Here are the instructions:
1. Make sure syslinux is installed
2. Get https://haar.student.utwente.nl/~julius/ahci.dsk.gz
3. Gunzip the archive and put it in /boot
4. Add the following lines to /boot/grub/menu.lst:
title           FreeDOS AHCI switch disk
root            (hd0,1) #copy this from the other Ubuntu item
kernel          /usr/lib/syslinux/memdisk #if your /boot is on a different 
partition, copy this file to /boot and put /boot/memdisk here
initrd          /boot/ahci.dsk
5. Boot the new boot item from grub (just press enter on the time & date 
prompt, there is no config.sys)
6. Run ahci_en

This should enable AHCI mode. You can verify this by running lspci or checking 
the dmesg output. I built this bootdisk myself based on FreeDOS and the program 
from Compal's website. You can also disable AHCI again with this disk.
I was able to do a clean Jaunty AMD64 install, do an update and run quite a few 
applications after I had done this. fsck doesn't find any problems at all after 
this and there were no strange crashes anymore.

I suspect that mainly Compal notebooks come with this mode set to no-AHCI, 
which is why there are so many reports of this problem with Compal notebooks.
For others without Compal notebooks with this problem, verify your hardware is 
in no-AHCI mode and try to switch it to AHCI mode through a similar tool. My 
bootdisk probably won't work.

I understand that AHCI mode also gives better performance, so this
should be an optimal solution. The problem with the ata-piix driver in
this kernel should still be considered a bug though.

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2.6.28-11 causes massive data corruption on 64 bit installations
https://bugs.launchpad.net/bugs/346691
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