After upgrading to iOS5, I was having the same issue for my TV shows and have resolved it by cleaning up sorting. I think this has to do with shows and seasons within them not having uniform sorting settings- which seems to confuse the iPad and IPhone. It took a little bit of time, but I removed all sorting on the shows EXCEPT "sort by show" and "sort by album" (where album is "Season 1" or "Season 2", etc). To save some time, you can select all shows within a season and assign the album name and sort preferences.
I also discovered the sorting on the iPhone and iPad want to default to the name of the episode (if episode ID - not track number - is blank). So, I went through and input episode IDs and now my shows group by show, then season, then sort by episode ID - just like we've been accostomed to until upgrading to iOS5.
Now on to figure out why my personal hotspot and wifi isn't working like it used to...