As a late follow-up, I had an external enclosure (Oxford Semiconductor) with two drives in it which I configured as a software RAID.
I then removed the RAID config and used SuperDuper! to create multiple bootable clones on a
single disk (leaving the other disk unused.) Worked perfectly and showed up all bootable partitions. Still can't explain what went wrong with the LaCie drive, but I'm happy with this for now