I installed a disk caddy with a PATA/SATA interface, and had booting problems -- grub would freeze up when accessing the disk. The disk worked fine as a disk, but when present, grub would freeze when accessing it in any way, even just tab completion on the grub command line! My BIOS did not allow selecting which disk to have first in boot order, and the caddy disk had precedence. Changing the BIOS presence/absence of a CD drive did not help. I had Ubuntu on both disks.
Oops, found some old notes, couldn't run off the caddy, needed to find a workaround to boot the first disk, then use the disk in the caddy.
This meant that I could only run the Ubuntu on the internal disk only if grub avoided the caddy disk completely!
A workaround is to boot off something like USB you can put before the hard disk(s). I could set grub up to run the installation on the internal harddisk, avoiding any reference to the caddy, and that succeeded. The caddy disk may then be mounted and accessed in a normal second disk fashion. There may be other grub modules to include which might fix the problem, but I didn't find anything which worked.