Yeah some of the episode ordering for Plex can be clunky, because of the way it pulls metadata. Follow what Zachariah said, but also verify that Plex is using the metadata from the source you find the episode ordering from in the shows settings. For example here's how some of the specials I have for the 2005 series show up, the numbers skip around a lot but Plex will still play them in their proper order if watching the series all the way through
