I'd just like to mention that this has only been a recent problem too. With BSP build 820 everything worked perfectly fine with Haali's Media Splitter and VSFilter. All MKVs/OGMs/etc played. However when the "better support for haali media splitter" and "more compatible with Haali splitter" changes were being added they actually had less Haali support then before. I recall that MKVs with more then one audio stream totally did not work, different subtitles, and lots of other things. All up until the last two builds everything but VSFilter playing VobSubs seems to work properly. Please fix soon :)
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