I may have your answer. You see, normally, an mkv has the streams in this order:
1. Video
2. Audio
3. Subtitles
Some groups, for some reason, reverse them:
1. Subtitles
2. Video
3. Audio
When the subtitle track has a higher position then the video track, it will sometimes not register. You can either
a) remux the file and put the sub track at the bottom
b) disable the internal MKV splitter and use Haai
Hope that helps
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