I think I found out why TV shows/seasons are disappearing at the end of the list in the iPad Video app!
In my case, I lost a TV show at the end of my list on the iPad Video app. My Artist fields were filled in correctly, the season numbers were correct, and the Episode ID fields were all unique. However, the Sort Album fields for my TV shows were incorrect. For every season of every show, the Sort Album field must be unique. The Sort Album field must also be identical for all episodes within that season.
I figured this out when I noticed the following symptom: If, when using Home Sharing, you are unable to find a TV show/season in the VIDEO app on your iPad, check to see IF ANY OTHER TV SERIES/SEASON IS LISTED MORE THAN ONCE! I bet you will find at least one duplicate, and that may be the source of your problem!
You see, each season of each TV series should be listed in the Video app only once. But if the Sort Album field isn't set properly, a single TV series/season may show up multiple times in your list. When this happens, the duplicate entries of that TV show will push other TV shows off the end your list. And that's why the TV shows at the end of the list disappear!
For example, I own several episodes of the fifth season of MythBusters, but I had 2 entries for Season 5 in my iPad Video app. I checked the episodes, and they all had "MythBusters" listed as the artist, with the proper season and episode numbers. However, some episodes had their Sort Album field set to, "MythBusters, Season 5" while others had the Sort Album field set to just, "MythBusters".
By setting all the episodes in that season to the same unique name: "MythBusters, Season 5", the duplicate Season 5 in my iPad Video app went away, and the TV series at the end of my list magically reappeared!
If you suffer the symptom listed above, make sure that every season of every show has a unique Sort Album field, and that the field is the same for all episodes within each season.
Good Luck!
Jonathan