I also tried doing a “Plex Dance”. That was a little weird. After moving all the files and doing the “Plex Dance”, I then moved the files back and did a “Scan Library Files”. After a short bit of watching the spinning icon, the display showed the proper number of seasons. But when the spinning icon stopped, the seasons display disappeared and the display just showed the episode count.
I am having this same problem. Directory structure is the same for the shows that show seasons and those that don’t. Can’t sem to find any options that make a difference.