I’m not sure what the issue is, but I’m pretty sure Plex recognized these seasons in the past. They are named correctly (SXXEXX) but stubbornly seem to not show up in Plex Media Server.
I’ve switch metadata reads to default to local files because I had one show I needed to manually include the metadata. Other than that, I can’t think of any other issues that would cause this problem.
if they are not appearing at all and there and nothing unexpected when you filter on duplicates then if you are on DSM 7 on your Synology I would check that plexmediaserver has permissions to the shared folder you have all your media in. I’m not a Synology expert but you may need to check the subfolders as well