Currently Being ModeratedJul 31, 2011 12:35 PM (in response to Andy MPC)
After some more digging it seems to be that way that when the hard disk is bootable then it fails. In order to test that is there a way to make a bootable drive un-bootable. My hard disk is bootable because the OS was initially installed on them and I used SuperDuper to copy it onto the SSD.
Currently Being ModeratedAug 5, 2011 6:45 PM (in response to Andy MPC)
Having no further clue on how to proceed I made a SuperDuper copy of the secondary HD, erased it with DiskUtility and Encryption on and copied the SuperDuper copy back onto to now encrypted secondary HD.
Now the disk is encrypted which was the goal all along.