How do I encrypt an external drive with FileVault 2 in OSX Yosemite
I understand that you're running into issues, so this is going to be more for others looking for info on this topic. Encrypting non-boot volumes should be a relatively easy process in OS X 10.8.x and later.

To encrypt a non-boot volume:


Right-click on the volume you want to encrypt
Select the Encrypt… command





When prompted, enter a password and (optionally) a password hint.




The drive will momentarily disappear from the desktop (to initialize the encryption) then re-appear.