Apparently .mkv is not supported, check here to find a list of supported formats http://support.xbox.com/en-US/xbox-360/settings-and-initial-setup/watch-dvds-movies
Whenever I play a movie from my USB drive it's either in the .AVI or .MP4 format. I know from experience .MKV is not supported, just find yourself a video file converter online and convert from .MKV to a supported format.
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