problems organizing videos in itunes/front row

I'm setting up my new iMac as a media server, and copying movie files, and tv shows over into itunes. I have used metax and lostify, and while they are great at what they do, i think my issue is with itunes.
One specific example is with Season 2 of The Office. Every episode has title, genre, show, season, artwork, etc. labeled correctly. But for some reason episode 4 doesn't not fall in line with the rest of the season in front row or in itunes. I have triple checked whether i added errant spaces or anything, but all fields are exactly the same as others.. yet they still don't show up correctly.
Are there any tips in how to organize videos more effectively. I have been thinking about just making sub folders within my movies folder, even though that seems dumb since i would then be rendering the TV Shows tab useless.

ANy tips?

as far as i know, you can use those video file types if you have the right codec installed (perian), and then organized withing the movies folder, you will be able to use them in front row. I think that they will not work in itunes, but i could be wrong.
On another note, i think that i am going to just start organizing all my videos under the movies folder. I really just want to add artwork to each, as the info summaries really dont add that much appeal for me, and its just not worth the flukey organization that itunes uses.