One last tidbit. I finally figured out what the IDE controller was and
why it was loading and being controlled by ata_piix. This board is an
Intel vPro board and it supports IDE redirection over LAN. Basically at
the firmware level it lets be remote mount an ISO image as if it was a
locally connected CD-ROM drive.

This virtual IDE CD-ROM drive is what is connected to the controller
that ata_piix is driving. So the system was behaving as expected outside
of the very slow boot.

So in summary. all that is needed to fix this bug is to change
CONFIG_SATA_AHCI= to 'y' from 'm'.

I verified it by making the change in
debian.master/config/amd64/config/config.flavour.*

I then rebuilt the lucid kernel, installed it and I am a happy ubuntu
user again.

-- 
Slow boot caused by SATA controller reset
https://bugs.launchpad.net/bugs/595448
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