Actually, the ONLY thing I can think of is my mobo has a built in Promise Technologies Ultra ATA100 controller host on board. And that is what my Ubuntu drive is plugged into.(And is set to be the boot devise in the Bios) The other drive on the main primary IDE channel are physically unplugged.

Primary master = XP (unplugged)
primary slave = empty drive for storage (also unplugged)
secondary master = cd burner
secondary slave = dvd burner
Promise controller = Ubuntu drive


This motherboard is an old Asus A7V classic with the built in extra IDE controller host.
http://www.anandtech.com/showdoc.aspx?i=1303