Comment 10 for bug 45989

Similar problem here.

I had Windows installed on my first HDD (Master) and installed GRUB in the MBR of the second HDD (Slave) so that it wouldn't overwrite the Windows boot loader. After changing the boot device priority in the BIOS, nothing booted and I had to edit the menu.lst manually. (I tried it again and again, every time I installed Ubuntu on a friend's computer, and it never worked.)

As far as I understand the problem (and I'm pretty sure I don't fully understand it, so it's just a guess), in my case the fact that GRUB is installed in the slave's MBR (which the installer knows!) is simply ignored, therefore the device numbers in the automatically generated menu.lst are wrong. If it's just that, it shouldn't be too hard to fix.