Another "me, too" for this bug. 
Ubuntu 9.04 64bit - SATA AHCI mode - ext4 fs
WD Velociraptor (ext4fs:  /, Swap, /Data)
WD Caviar Black 1TB (ext4fs:  /home)
WD 640GB (ext4fs: /Backup)

I recently built a new system using an EVGA 760 Classified MB, i7
920cpu, 12GB triple ch DDR3 and 300GB Velociraptor. I installed the OS
after setting the BIOS to SATA AHCI mode (needed hot swapping
capabilities). Everything worked fine for about 1 month until last
night. I was doing a very large (200GB+) grsync backup of my /home
partition to my WD640GB backup drive. At some point in the backup the
system froze. No combination of keyboard tricks (ctl+alt+backspace, or
alt+print screen+REISUB) would restart X or reboot the OS. I had to
resort to killing power.

On reboot, the one of my BIOS screens reported "Port 00:" during what I
will call the AHCI check. The Velociraptor system drive would not boot.
When, I went back into the BIOS setup, I saw that the BIOS did not even
see the Velociraptor. I assumed the crash and hard power down had
corrputed some critical system files. I removed the Velociraptor boot
drive and replaced it with a WinXP 64 boot drive (also set for AHCI
mode) and was able to boot up a Windows system with no problem. I then
tested the Velociraptor with SpinRite 6 and its a good drive.

I decided to try and reboot the Ubuntu system by changing the BIOS SATA
setting to "IDE" mode. This worked. Ubuntu was able to start after it
found a few errors on the / partition, corrected them, and finished
booting. Ubuntu 9.04/64 now seems to be working fine in "IDE" mode.

After reading through this thread, it seems that I have been bitten by
this AHCI bug when I was doing the very large rsync file backup;
although, I have to add that this wasn't the first time, I did such a
large backup on this new system without problems.

-- 
ata timeout exception with ahci libata driver (was with 2.6.28-11, but i 
confirmed it affewcts previous kernels too)
https://bugs.launchpad.net/bugs/352197
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