Can you tell us wich decoders (filters) are used to decode the file and also, and the most important, the splitter you use ? You can find them when playing an MKV file via rightclick->options->filters->advanced. Please post here.
Do you use internal or external subtitles ?
Are you sure you use BSPlayer's internal subtiles rendering engine, or vobsub/vsfilter ?
LE: tested with both types of subtitles, no problem in here, using CoreAVC, AC3filter, Gabest matroska splitter
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