VLC plays the MKV file fine but toward the end (last 1, 2, or 3 seconds depend on which MKV file being played), VLC froze. It still responses to clicks but doesn't do anything. Pressing X just minimize the window but doesn't actually exit. The only way to exit is to kill via process manager.
I'm able to find some MKV files where the above problem doesn't exist. However, most of my MKV files have the above problem. Seems to happen on MKV files with multiple audio tracks. When it "freeze" as describe above, the "Audio-->Audio Track" menu only show 1 audio track (Disable and TrackX) but before the froze, there are 2 audio tracks (Disable, TrackX, and TrackY).
Update: The Tools-->Messages window doesn't show any error message.
Versions with the above problem: 1.0.0, 1.0.1, 1.0.2, 1.0.3
Versions without the above problem: 0.9.9.
Confirmed problem on the following OS: Windows Vista and Windows 7.