Intro detection and other new features only work if a show is using the new agent.
The Plex dance did work because it clears the matching of a show with the old agent. If you re-add the show later, it will be matched with the current default agent of the library (which is the new one).
The first XML is showing guid="com.plexapp.agents.thetvdb://72108/16/15?lang=en. This is the old TheTVDB agent.
You seem to have switched the metadata agent of the library to the new agent, but have never performed Refresh Metadata of the whole library.
Only after this process has been completely done, the conversion of all the existing shows in the library is actually performed.
So, Refresh Metadata of the whole library.
