Depending on drivers in Linux distribution like Ubuntu, mkv files might not be running smooth.
Install the nvidia/ATI drivers via system > administration > hardware drivers
Install the libvdpau1 package via synaptic package manager or open a terminal and type or Code:
sudo apt-get install libvdpau1
install smplayer (a nice frontend for mplayer) via synaptic or in a terminal: Code:
sudo apt-get install smplayer
After they install, open smplayer and in the toolbar, go to options > preferences…click the video tab and for “output driver”, scroll down the list and choose “vdpau”
Run .mkv file in smplayer, it should run smoothly now.
More on the topic: http://ubuntuforums.org/showthread.php?t=1514513