I'll give this a bump because I am having the exact same issue and frustrations. There are a handful of movies that I have reclassified into a specific genre and it seems everytime I open iTunes it moves them back into the genre they were originally in. Just like the OP though, when open "get info" for each movie it shows then under the genre I want them under - iTunes just puts them under the different genre.
For example, Alice in Wonderland was classified under "action and adventure" when I originally downloaded it. I moved it to the "kids" genre, but iTunes keeps moving it back to "action and adventure". Other examples, Star Trek Into Darkness get's classified under "action and adventure" even though I reclassified it under "sci-fi and fantasy" (and oddly the other Star Trek is classified and stays under "sci-fi and fantasy"). Also, iTunes keeps putting Madagascar 3 under "comedy". I'll admit that it is a kind of funny movie, but I would still prefer it be classified under "kids".
Those are just a few examples. I really don't see the point of being able to make changes to the classification of the movies if iTunes is just going to change it back for you. The only thing I am wondering is that if a movie has been downloaded on to a device before you make the changes in iTunes, and then you sync the device after making the change in iTunes - maybe that causes some confusions. Would iTunes look at how the movie is classified on the device and then sync it accordingly? Not sure, but if that is the case, I do wish changes made to the library would superscede changes made on a device.
Not a huge deal in the grand scheme of things, but if there is a solution I'm all ears. Any more light people can shed on this would be much appreciated.
Matt
P.S. I am on a PC if that has any bearing on the matter. Noticed this is in the iTunes for Mac category