I don’t use this subtitle type myself as I’ve chosen to use external srt but in the absence of anyone else giving a suggestion I do wonder if the fact they are registered as language unknown causing some problem.
Have you tried taking one file that you know does not work now and setting the language to say English ? Then do a plex dance on the file including analyse of the media (probably overkill but worth doing) and see if it helps. From what I remember closed captions are embedded directly in the video stream which is why setting the language on the video stream itself might help.
Good luck …
