have you tried syncing them with your iphone? after hooking up to your iphone you should have tabs stating apps, photos, music and videos. ( I am not at my home computer so I can't bring it up and look to be certain.)
go to the videos or movies tab and click on the movies you want to sync or just sync them all.
but I also have run into the problem where a movie will not sync at all. Devilman for one that I got from my son.
good luck
I just seen this question and answer on another post and I did forget this one minor thing. right click the movie and convert to iphone. hmm...maybe i forgot to do this with Devilman.