Here is a solution that works for me under Mountain Lion. WARNING: Use at your own risk. I have not lost any data, but since the solution depends on Disk Utility fixing some problems produced during the solution, I would not try this on a disk that is not safely backed up.
I have a MacBook with an FileVault encrypted internal disk "IntHD" and several large (e.g. 3 and 4 TB) external USB 3.0 disks, all of which have 4096 block sizes. I used Carbon Copy Cloner to create a bootable clone of IntHD on partition "IntHD Clone" on external disk "ExtHD". When I boot from "IntHD Clone" and turn on FileVault, I have the problem seen by singerkd above. One sees "Estimating time remaining …" forever, or if one enters "diskutil cs list" in Terminal one sees that the conversion is "Pending" not "Converting".
Here is how I solved the problem:
1. Reboot from internal disk "IntHD" and run Disk Utility Repair Disk on ExtHD and all its partitions. If Repair reports problems, run it again until no problems are reported. If you reboot from "IntHD Clone", FileVault should now found to be turned off. (Obviously, you should replace "IntHD, "IntHD Clone", and "ExtHD" by the names of your own disks and partitions in the following procedure.)
2.Reboot from internal disk "IntHD" and in Terminal, type:
diskutil corestorage convert "IntHD Clone"
(Note: the quotes around "IntHD Clone" are needed.)
You will see some output saying the conversion is complete.
3. Run Disk Utility Repair Disk on "InHD Clone" on ExtHD.
One will likely get errors such as "The volume … found corrupt and needs to be repaired." and "Incomplete or inconsistent CoreStorage Physical Volume Set". (Note: Read WARNING above. You really need a good backup in case something goes wrong at this stage.)
4. Reboot (from same internal disk "IntHD"), and run Disk Utility Repair Disk on "IntHD Clone" again. Repeat until no further errors are seen. To be sure, you should run Repair Disk on the whole ExtHD disk. After one or two passes, ExtHD should be error free.
5. Reboot from partition "IntHD Clone" on the external disk "ExtHD", and turn FileVault on.
6. Reboot from "IntHD Clone". Under System Preferences Security & Privacy, it should now say that FileVault is turned on and it is "Encrypting …" with "X hours remaining".
7. Reboot from internal disk "IntHD" and get on with your life while FileVault Encrypts "IntHD Clone".
Note that the conversion to an encrypted disk only happens whenever "ExtHD" is attached to your computer, so if you just put ExtHD on the shelf at this point, it will not be properly encrypted, you need to leave it attached (or at least reattach it when convenient) until the encryption is complete. One can monitor the status of the encryption of "IntHD Clone" while running from "IntHD" by opening Terminal and typtyping
diskutil cs list
In the resulting output, look for "IntHD Clone" and find "Size (Total)" and "Size (Converted)". Initially the latter will be much less than the former and it will also say "Fully Secure: No", but they will be the same once the encryption is complete. Once complete it will also say "Fully Secure: Yes".