vlc does not use direct show, it uses its own internal codecs. to get the best playback of x264, (the mkv’s) you will need to get http://www.coreavc.com/ which is not free but is much better or try downloading http://ffdshow-tryout.sourceforge.net/ in ether case use media player classic from here http://sourceforge.net/project/downloading.php?group_id=82303&use_mirror=superb-east&filename=mpc2kxp6490.zip&22646901
you might also need ac3filter http://ac3filter.net/project/1/releases