I have a Matroska file I encoded using x264 that experiences momentary skipping at a given point in the file. Putting the video from the Matroska file into an MP4 file (using mkvextract and then mp4box), the skipping does not occur. Also, the skipping does not occur in playback of the Matroska file using VLC.
This problem occurs on both a dual-core Intel Mac mini 1.66GHz, as well as a PowerBook? G4 1.67GHz - neither of which shows a lack of available CPU cycles in Activity Monitor during playback.
The problem occurs shortly after the 5:00 mark in the example file, and sometimes causes the video to freeze for up to a few seconds, though usually it's only for a few frames. The video frames do individually play back fine by stepping through the file with the arrow keys.
There doesn't appear to be any debug output, or I would include it. Please let me know if you need any more information.
Example File [68.8MB]:
http://www.monkeyvoodoo.net/~eclark/Ichigo_Mashimaro_01.mkv