I think other users have said it, check your scanner and agent.
I have been using the Plex TV, series scanner, and the Plex TV series agent.
One day I went in because a show was not showing up properly, and I switched my scanner to Plex series scanner, and that locked me into… I think it was the movie database as far as agent.
It basically locked me into that new setting, too, I could not switch back to Plex TV series.
I ended up doing a troubleshooting dance. Eventually I was able to set my scanner and agent back to the default setting. And after that, I was finally able to get that show to show up properly, but all during the time I had Plex series scanner, it went into my complete TV library and it re-ordered every single show.
I have a couple of shows that have viewing orders that are not the same as when they originally Broadcast the show, for example, space above and beyond, and of course firefly.
Also, Farscape.
The first seasons of those shows actually the only seasons for a couple of them, were completely broadcast totally out of the intended order.
I have finally found ways of setting that properly within the shows that are affected, you have to choose absolute, ordering under the advanced settings under edit. In fact, I just checked my fire, fly sorting, and it was totally bogus, so I got into the advance tab after I selected absolute ordering everything fell right into place.
The thing that bugs me is, I even have the episodes numbered correctly in their folders, and still, if I use the default scanner, it will try to show the broadcast order