When running autoorganize against Always sunny season 14, it names 7/10 episodes as "Episode #S.E" and the other 3 are named correctly. All 10 files are named with the same pattern.
I cloned autoorganize and launched with debugging against a new clean emby portable instance and it names all of the files correctly, so I made sure to match settings between installs and it still consistently does this.
Both instances are using 1.5.6.0 autoorganize and emby 4.4.2.0