Agreed, that is my understanding too. Because of the nature of my PC my main hard drive is SATA and the 2nd is IDE which is linked in with the IDE DVD/ROM drive as there is only one IDE input on the motherboard.Strange error, if you refer to the partitions with UUID, it should work even if you swap the connections. Are you sure there is good electrical contact? Maybe you have to unplug and replug the disks again.
It has happened before so the above slightly strange configuration may be the cause.