I just tested with this structure (the library points to test_tv) and it worked as expected:
test_tv/
└── Red Dwarf (1988)
└── Season 01
└── Red Dwarf (1998) - S01E02 - Future Echoes.mkv
You’re not just swapping back and forth between the legacy scanners/agents and the Plex TV Series/Plex Series scanner/agent, are you? Nothing good will come of that. Stick with the new scanner and agent, it will (can, obviously) work.
Can you show a screenshot of this page of your library configuration?
Finally, switch back to the current scanner/agent (if not already) and perform the Plex dance on the Red Dward series. Then, collect your server logs and upload them here.