I see there are two topics with this question. I am responding to this one, because it was higher up.
Anyway, I think this is the same issue that people have been having for awhile with iTunes library sharing on the iPad. If you search for it here, or on the Apple discussion forums, you'll see all kinds of things about it. Anyway, I too had this problem with my iPad, but after reading other solutions, I was able to fix it for my iPad, finally! I'm not 100% sure it will fix the Apple TV issue, as I haven't upgraded yet (waiting for JB).
So, it seems to be an issue with tagging. For some reason, the iOS sorts in a weird order, looking at album field, artist field, episode id, "sort name", etc. Here is what I did, following others' advice, that fixed it. It basically involves a lot of re-tagging, but it is worth it. I know you might be thinking that you have it all tagged correctly. I thought so too, but it got weird.
1. Make sure every episode has the same thing written in "Show" field, "Artist" field, and "Album artist" field. For ex., "Family Guy".
2. Make sure every episode per season has the same thing in "Album" field, like this: "Family Guy, Season 1". This is how iOS will group season episodes together.
3. Include "Episode Number" for every episode in the correct order..
4. Include "Track Number" for every episode in the correct order, as well as total track numbers. Ex., "1" of "22".
5. Trickiest one: Every episode must have a UNIQUE "episode ID" within a season. Meaning, you can't have the "episode ID" number of "Family Guy" Season 1, Episode 4 as "4", and have the "episode ID" number of "Family Guy" Season 2, Episode 4 as "4". You can repeat the "episode ID" in another series, but not within seasons of the same series. I hope that makes sense. For me, I named every "episode ID" for each show with this convention: "S01E04", S02E12", etc.
6. Do not put anything in the "sort" fields, like "Sort Artist", "Sort Album". Let iOS use the other information.
So anyway, sorry for the long winded response. I hope this helps. It's a pain in the ass, but it worked for me. The best thing I used was Dougs iTunes script "Increment Number Tags". It takes care of "Track Number", "Episode Number", and "Episode ID" in batches.
Good luck!
-Lilscoy22