Did you do the Plex Dance? Most likely Plex has already matched the show when you first created the library. It likely thought it was a duplicate of another show you have, so those episodes are improperly combined into another show. No matter how many times you rename a file or correct the layout, or change the names, it will NOT un-combine these shows, thinking that all you did was a slight filename correction.
To fix this, you either find the show this one got combined to (using a filter for Duplicates) or (much easier) just do the Plex Dance. This makes Plex forget the show was ever matched previously. Then, the next time you scan for media, it does the “discovery and matching” process all over again. Since your layout looks fine now, you just need to trigger this discovery process, and you do that via the Plex Dance.
Did I mention Plex Dance enough times yet? 
