The question in this is where's GRUB installed and how is it configured.
If you disconnect all the disks exept Ubuntu it will boot,no problem,but if all disks are connected,it won't boot.

This in fact is that GRUB is counting your hdd's and comes with the wrong hdd for Ubuntu so it can't boot.
You have to edit menu.lst so it points to the right hdd for ubuntu and probably your fstab too.

That's why I advice to leave all the disks connected so they are properly assigned in GRUB and menu.lst and fstab as well.

Try sudo fdisk -l to find out how your disk are ordered and alter menu.lst and fstab to correct things.