Having the same problem with all the movies I downloaded from the Hangover 2 to the Rise of the planet of the apes plus more, Been working with someone for about a week now maybe longer to try different steps.
The steps they are having me do is something I already tried or I know it has nothing to do with it but I will do it for them.
What the problem is ( and something happened like this a while back with everything) the extras are not moving to the "Movie" folder in the itunes folder, they are still in the download folder and moving them wont help because they dont have the correct names to the video file. each file is in a flder with a name like Hangover II extras (something like that) and inside it the video file just says "download.m4v" and until its named correctly it can not play thru itunes video or Apple TV, once they get named they may work after that but im trying to get the file names so I can try it with the hangover 2 since that only have 4 videos. Right now they want to reset my password and im not sure why but it the email I got today, but trust me it happening on 2 different computers and even 2 different accounts on one computer, I tried it on a new fresh user account that I created and still same thing all files in the download folder with not names to match each file.
The problem is with the last itunes update because the other movies I downloaded had extras and they play fine and all are moved into the Movie folder in my itunes folder. now if I click on each folder and play each video file they will play but I just cant do it from itunes or my apple tv I have to go into my folder and search my download folder and play each one manually.
when this happened while back it was doing the same thing but with everything and when I used a earlier version of Bonjour for some reason the problem went away but I did try that now and no luck.
all I know is I want the names of each video file so I can test my theory out and im sure it will work just waiting for them to finally listen to me.