Thanks for the post. Neither drive was ever connected to the PCI IDE controller, and I've never booted from the controller. I have the boot drive set as #1 to boot right now, and none of the other connected drives (all to the Highpoint RAID controller) have bootloaders on them. The trouble is, the system isn't even booting into GRUB; if it was, I'd know how to repair it. I've tried reinstalling the bootloader to the drive but it hasn't helped.
That's what I can't make sense of: I have it set first in boot order, I've verified that GRUB is intact, but the machine refuses to boot from that (or any other) IDE drive. I know it's not the drive, so I figured it was the motherboard crapping out.
To your last point, I wish
it was a GRUB or BIOS config issue; those are easy to solve