Wrong Metadata for new shows

You have Plex TV Series for both the scanner and the agent, correct?

If so, I do not know why Plex is not recognizing the show correctly.

One other thing to try:

  1. Create a second TV library.
  2. Move the show out of the current library.
  3. Perform the Plex Dance (scan, empty trash, clean bundles)
  4. Place the show in the second library.

If Plex correctly matches the show in the second library, then, as @OttoKerner mentions, something may have gone wrong if/when converting the original library to the new Plex TV agent.