Did you ever test another player? If not, just try playing one of the mkv's in MPC-HC or VLC completely outside of WMC and Media Browser and see if it freezes.
If it doesn't freeze, then it rules out the hdd as a potential issue.
I don't use LAV or Shark007 or any other 3rd party splitters/codecs and files play fine (only have 2.1 speaker setup). Try MPC-HC stock install, if there's no playback issues, then try setting it up to use LAV and see if it still plays fine. If you have success with any of these, then that can point you in the right direction.