Disc Season Episodes are Specials according to TvDB

[pshanew]

Did you perform the full Plex Dance?

The Plex Dance ™

The purpose of this is to remove all cached metadata and xml data for an item that Plex usually keeps. This helps when you want to “start from scratch” for particular item move all files for the media item out of the directory your Library is looking at, so Plex will not “see” it anymore scan the library library (to detect changes) empty trash clean bundles (in menu next to server name, when accessed under ‘More’) double check naming schema and move files back scan the library Support articl…

In your description above you left out an important step: Clean bundles. Unless you’re positive you did it already, I’d recommend going through the full dance again. And make sure to set the show back to DVD order.