I don't think that!
But anyway, you can still use the manual way. Use on the Dune HD remote the "Subtitle" button and select the listed subtitle tracks to find out which are the correct one. Easy task
Can you explain this point? Subtitles from Internet, other disc or ...? All tracks in an MKV file have an PTS (Presentation Timestamp) to sync the components. Adding things from anywhere can be a problem if different timestamps are used.