I have confirmed that the same behaviour is seen in Intrepid (20081009 /
AMD64 Server).  My workstation has the following hardware -- which
differs in chipset than the original with the disks listed in physical
order:

MB:  Abit KV8Pro

PATA1:  1x 80GB and 1x 120GB disks
PATA2:  1x DVD drive
SATA: 2x 120GB disks

I have attached the output of some commands (uname, lspci, dmesg, fdisk)
from Intrepid, as well as from Gentoo and GParted Live for comparison.
It seems that in Ubuntu, Grub is seeing the correct order for the disks,
but the order the the kernel provides to it during the install is
incorrect.  This probably only affects systems that have integrated PATA
and SATA controllers provided by a single chip with both types being
used.

My guess is that Ubuntu is the only one (of theses three atleast) that
is solely relying on the new 'libata' module.  The others still have
/proc/ide populated.

Let me know if there is any thing else I can provide for you.

** Attachment added: "Not fixed in Intrepid (20081009)"
   http://launchpadlibrarian.net/18376640/output.zip

-- 
Grub installs to wrong drive's MBR in default install. No way to change in 
standard installer.
https://bugs.launchpad.net/bugs/46520
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