I know this isn't in the spirit of things. It is a fudge.
If you have any MKV movies with subtitles tracks that don't show when playing under LMCE, there is a way to extract the subtitles track as a separate .srt file, meaning they should then appear.
0. Install "mkvtoolnix" if you don't already have it.
1. Probe the file for the track information...
mkvmerge -i SomeMovie.mkv
Track ID 1: video (V_MPEG4/ISO/AVC)
Track ID 2: audio (A_DTS)
Track ID 3: subtitles (S_TEXT/UTF8)
Track ID 4: subtitles (S_TEXT/UTF8)
Chapters: 74 entries
2. Verify which subtitle track you want to convert (I do this using VLC on another computer, maybe there is a way to do it on command line). Let's say we want the subtitles on Track ID 3
mkvextract tracks SomeMovie.mkv 3:SomeMovie.srt