In case the additional information helps (not sure that it does), the issues started happening with the “PlexMediaServer-1.16.4.1469” update on macOS (Catalina beta 5). I downgraded the PMS to “PlexMediaServer-1.16.3.1402” and the issue went away.
And yes, the issue seems to be mostly there with MKV files. But then again, Plex seems to have a lot of issues with MKV files all the time - does not display subtitles from MKV files sometimes, for example. Other times, it will show the subtitle fine. I do realize that MKV is a wrapper format and that the issue might be elsewhere but just letting you know.
My client/player is the Roku Plex app but I don’t know if the issue is on the client side since downgrading the server did fix the issue for me.
