I’m also having similar issues with subtitles, but with the web player. I didn’t receive any support with my problem but looking into it myself I figured out it was happening only with mp4 files. So I just switched to mkv formatted files. Perhaps you could try different combinations of files and subtitles formats for your issue.
Overall I think plex needs to redo their whole subtitles code. The support is spotty at best, issues with disappearing subtitles cropped up for people over the years, again and again. Some subtitles just crash the streams(in the web player but not the windows app) if they have some weird formatting in them, like for anime. It’s all a mess imho.
While googling for my issue I saw plenty of similar problems over the years and the only advice that people got was just burn in the subtitles. Which is too big of an ask for me.
