The subtitles you were seeing probably were rendered by VobSub (or Vsfilter). If you installed it by your own will, then is OK and you could disable the subtitles from the green icon in systray. If you didn't installed, then it came from a codec pack. If you don't need it, uninstall it.
On the other hand, if you have MKV with internal and external subtitle you may experience some problems, especially if one of the subtitles are in vobsub format. If this is the case, in options->preferences->filter management, enable both options. Can you also tell us if you use Haali media splitter for MKV ? (play an mkv->options->filters->advanced and click on the one named "source"). If you install Gabest mkv splitter do you have the same problem ?
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