From my own experience and from reading a lot about it I've learned that VLC has some problems playing x264 encoded files, as it is not using a codec for decoding the movie.
I've never had any problems using vlc for years with xvid encodes. But since I downloaded more blurays the problem became very obvious.
The movie just is lagging very strongly and playback is just "bumpy", though the sound isn't affected at all.
Because of that fact I tried out Media Player Classic and it is actually equally good. The .mkv files play flawlessly using the x264 codec.
Both, player an codec (ffdshow) can be downloaded at
x264.nl.
VLC is amazing for playing movie files of all kind, but if you are experiencing those playback problems aswell, just keep MPC in mind :)