Here's a workaround at least for my case without any severe modification of the 
system.
1: Make sure the bootloader is installed on the boot HD whether it works right 
or not.  Manually install if you have to with find root and setup in grub off 
the live cd (I'm not putting those instructions here myself but they're easy to 
find)
2: Boot to the bootloader which will fail because the menu was configured 
wrong.  Use the GRUB command line and the built in editor to find out what the 
real hd#'s are, using trial and error for windows (I recommend changing root to 
rootnoverify and deleting the maps if windows is on hd0) and "find 
/boot/grub/stage1" for ubuntu.  Write these down.
3:  Use GRUB's built in editor to temporarily fix the boot menu option for 
Ubuntu and boot it.
4:  In Ubuntu edit /boot/grub/menu.lst and manually fix the boot menu options 
to the hd#s as they are on boot.
5:  Manually install the GRUB bootloader as in 1, ignore the fact that the 
hd#'s are different than they are at boot, the menu.lst is already fixed this 
is just to get the bootloader updated.
6: Reboot and test.

Here's my own config: Asus A7N8X-E with an add-on PATA card (I'm too
lazy to find out which).  The windows install is on 5 partitions across
2 drives:

Onboard PATA controller:
hd0 in GRUB hd2 in Ubuntu
1 Windows Install
2 Programs

Second PATA controller
hd1 in GRUB hd0 in Ubuntu
1 windows pagefile
2 documents and settings mapped directory
3 file storage

hd2 in GRUB hd1 in Ubuntu
Onboard 3rd-party SATA fakeRAID controller (in non-RAID)
1 linux
2 swap

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