Have you already done a Plex Dance since you moved all those things around?
Library folder needs to be /Media/TV shows/ for Plex to properly recognize stuff.
I can only guess that Plex had initially mismatched the files due to the perceived wrong structure – when you shifted things, Plex still remembered that those files are known and had previously been (incorrectly) matched. The way the agent/scanner is build, it’ll try to maintain existing structures – the Plex Dance is “designed” to make Plex forget any previous bad associations.
