Comment by bigstrat2003

I don't recall the folder names being different, but by default Jellyfin uses different metadata providers than Plex. That means that things like numbering of specials (think BSG and the webisodes), or shows which have a different aired vs DVD order (i.e. Futurama) might differ between the two. For those, you have to either tweak your episode numbers or just tell Jellyfin to use the metadata provider Plex does (which is what I did for those edge cases).