Comment 86 for bug 8497

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