I had the same problem on my mede8er with some mkv files: a blank (black) screen, but i could hear the audio. Some mkv files didnt work at all ("invalid file").
I tried the solution from the opening post, but the .CMD file didnt work. The cmd file says that it requires mkvtoolnix 4.1.1, but the downloadlink from the post is mkvtoolnix 4.2.0, so maybe thats why. So i now i fix my files manually in mkvtoolnix 4.2.0.
Here is a screenshot with instructions:
http://i52.tinypic.com/rmtsn7.jpg Its dutch but the layout for other languages is the same so it will be useful for non-dutch too.
that cmd don't require 4.1.1, in principles can be done to work with any version.
it is just a batch script.
@Nosoul is right, use v4 if is fine for you