Exactly the same problem here. TV Shows mess on the iPad started with IOS5. The mess on AppleTV started with iTunes 10.6
I have all the latest gear with all the latest software.... If Apple keeps ignoring major bugs like this one I'll probably switch back to a MS based setup
Bad, bad, bad... please Apple fix this now!
Do you have any better luck with that if you update to iTunes 10.6.1.7?
From the notes for the release:
iTunes 10.6.1 provides a number of improvements, including:
• Fixes several issues that may cause iTunes to unexpectedly quit while playing videos, changing artwork size in Grid view and syncing photos to devices.
• Addresses an issue where some iTunes interface elements are incorrectly described by VoiceOver and WindowEyes.
• Fixes a problem where iTunes may become unresponsive while syncing iPod nano or iPod shuffle.
• Resolves an ordering problem while browsing TV episodes in your iTunes library on Apple TV.
This is what has worked for me. (And it shows that Apple has inconsistent implementations for sorting/presentation of TV shows across iTunes, the Remote App, Sharing on the ATV and Sharing on the iPad.)
Set these items in the "Get Info" dialog's tabs:
Video : Show - set for all episodes of a show to the same value.
This is sufficient for iTunes to group the episodes.
Info : Artist - set for all episodes to same value used in Video : Show
This is required for the iPad to group the episodes.
Info : Track Number - in correct sequence for each episode
I don't know if this is necessary. But it is where I started so I've got them all set.
Video : Episode Number - in correct sequence for each episode
This works for iTunes to display episodes in the correct sequence.
Info : Name - (optional) The episode's title. (This defaults to the file name imported.)
Video : Episode ID - set to same value as Video : Episode Number for each episode
With this field left blank the iPad sorts/presents the episodes alphabetically based on Info : Name
This is a rather ridiculous requirement of redundant data entry. And it clearly shows that no one at Apple is tasked to ensure that listing iTunes video content operates consistently across all the platforms which can present/display a common data set.
Please see my response here, hopefully it will help you get it sorted out, there are so many different variables that come into play with this situation it's absurd (come on, Apple devs make this easier on us!)