This is a bit weird. I think there's an iTunes OS X bug involved.
I wanted to control what TV shows went to my iPhone. My son wants to go to the polls with me early tomorrow, and he will need entertainment if we have a long wait. (Minnesota polls, however, are extremely well run. Waits are unusual.)
There are a lot of controls on what Music goes to the iPhone, but, oddly enough, fewer controls for space hogging TV shows.
The Library "checkbox" selector method breaks down when one has multiple devices -- those are library settings, not user or device settings. There are checkboxes for Movies that are device specific, but not for TV Shows.
One trick is to choose to sync "unwatched" episodes, then use the context menu "set new" option to mark watched episodes as "unwatched". (The new/watched term incongruity is a bug.)
Another is to follow this author's advice: Syncing the Next n Unwatched TV Shows to your iPod, AppleTV or iPhone using iTunes.
What worked for me was to create a simple playlist of the TV Shows I wanted and to use the "Selected playlists" option in TV Show sync.
Obvious in retrospect. Here's the odd part though.
When I first created my Videos folder, it didn't show up as a playlist I could select -- maybe because it also held some home movies. I created a smart playlist of an series of TV shows to see if that would work better; when I next checked BOTH appeared as playlists I could check.
Anyway, the Simple playlist approach works fine for my TV Shows. That should get Tim through the voting wait.