A point you made earlier ... scanned newest 52 renames..., Are these renaming after PMS has scanned them?
If so, did you remember to “Plex Dance” them out and back in so it picks up the name correctly the first time? If you didn’t, PMS is still hanging on to the incorrect information in the DB. It will associate the new, correct, name with the previous ‘unmatched bad name’ and not list it.
If that’s the case (it HAS to be simple like this), are you using a tool like FileBot or TheRenamer to ‘rename and move’ simultaneously?
When I process new video, however I rip it, I run it through FileBot. My movie template for FileBot puts it in the directory structure how I want it. There’s no reason you can’t do the same. Yes, it can be automated too 
My FileBot template for movies is as simple as /syno/movies/{n} ({y})/{n} ({y}) . I hand edit the extras (adding the -tag as needed and moving in manually.
My template for Series, which Sonarr also uses, /syno/tv/{n}/Season {s.pad(2)}/{n}.{s00e00}.{t}
macro names:
n = name
y = year
s = season
t = episode title
.pad(2) = directive to pad the season number to 2 digits (leading zero fill)
A possibility?
