This is how I fixed it:
First, in the episode ID field, enter the season+episode number--numbers only. E.g., the Lost season finale would be 322, not 0322, not S03E22, and definitely not the episode name--that goes on the first pane.
Ensure that the show, season # and episode # fields are completed.
Select all episodes, and ensure that Name, Album, Album Artist, and Artist fields are identical. While you're at it, add artwork too.
It was tedious, but I now have an impeccably organized video library on AppeTV.