I have the same issue with Ubuntu Dapper 6.06 LTS.  My equipment spec is
as below:

ASUS A8N-SLI Deluxe
2GB DDR RAM
4 x Hitachi DeskStar 400GB SATA drives running on nForce4 SATA chipset as 
individual drives
AMD Athlon64 3600+ (2.2GHz, running stock speed)
Windows XP is running on the real first drive.
Ubuntu detected the 3rd drive on the board as the first, and installed.  Caused 
Grub not to work without manually selecting the 3rd drive at boot.  Of course, 
XP cannot be booted because Grub has the drive order wrong.

I'd like to avoid lilo but it looks like I cannot.

-- 
grub guessed BIOS disk order incorrectly
https://launchpad.net/bugs/8497

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