I know this is an old thread, but I'm pretty sure people are still having this issue as I have had/have. I would like for any movies (*.mp4) that I have on my computer to show up under the "Movies" option on my iPad, so that I could apply the artwork (movie cover) to the movies. I've seen that some people were saying to right click the video you have & click get info > options > media kind, and change the setting home video to movie or movie to home video. Once again I prefer movie for artwork reasons. When I tried this method, it does something to the video that renders it useless. After you have changed the media kind, the video does not play. It will display an "O" and won't play.
Even if I have downloaded (Movie Name - Season X), from the same source/website, which could include multiple mp4 videos, when transferred to the iPad via iTunes, some end up under the movie category and some end up under the home videos category.
I have found that when using iSkysoft Video Converter to re-convert the already mp4 videos to mp4 again, all the videos will now show up under the "movies" tab on the iPad. I still have no idea as to why this needs to be done & I would have thought there would be something that could be changed via "right click" within windows to prevent this problem.
I am currently running Windows 7 x64 and using the latest version of iTunes (12.5.x), but have noticed this issue for as long as I can remember.