I have two SSD disks with Ubuntu 14.04.02 on both. They don't share the UUID or anything, and they are never plugged at the same time. This is a new disk I got last month and did a fresh install.
Here's what happen:
Plug only disk 1, everything works fine. I can boot and no errors occur
Unplug disk 1, plug disk 2 and I can boot this system too
Unplug disk 2, plug disk 1, now disk 1 can't boot anymore. Depending on what boot entry (from the motherboard) I choose I get a "can't find such device", "grub rescue" or "insert media" error. I tried booting using the (U?)EFI option and it also doesn't work. It's not a boot priority problem, it just stops working.
After I run boot-repair on disk 1 it starts working again.
My motherboard is a http://www.asus.com/Motherboards/P8P67_LE/ and there's also no "Fast boot" option on the bios.
It's like it's caching the entries with the UUID or something. I also have two options stuck on the BIOS menu. They are from previous installs like "Ubuntu" and "Windows Bootloader". They show up even when no disks are plugged in.