Does the BIOS recognise the other IDE controller? Is there any reason why you can't use the primary IDE channel on your machine.

EDIT: My main machine boots off a SATA drive and that works because I've got the SATA chipset driver compiled into the kernel. Maybe you didn't compile support for your IDE controller in. Can't offer any more help right now as I'm about to leave work....
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Cheers,

Andy M