Next time try moving them with lmce.
So I just had 4 movies to move around, so I go to the web admin, Files and Media sync, navigate to the directory in the left column, and then click on the file in the right frame, then click on Move...
In the pop-up, I move around until my directory appears and click the choose destination button and the file is moved.
I do this for each one.
Then I go back to the Files and Media Sync and call up the file to see if the Media Sub-Type field stuck. Guess what? Nope.
So if I move them by hand or move them via LMCE, my media sub-type field still clears itself. Now that's a PITA ;-)