mkv playback problem

[socal500]

I did not want to post this in bugs as Im not sure what the cause is. Let me start by saying I have created quite a few mkv files, all which playback perfectly on VLC. Today I created an mkv but playback has a strange characteristic best explained as a surging in the video. Its almost like the video slows down then speeds back up. It gives the appearance of slow framerate. This mkv was created like any other I have. What really confuses me is that I took this same mkv and just remuxed it to m2ts, so in a nutshell I just changed the container correct? Well the m2ts plays perfectly without the surge characteristic. What do I need to be looking for here?

Also.. this is using VLC version 0.9.4 and 0.9.2 on Vista and XP. I should also note that the mkv file will play fine on windows media player classic without the surge problem. Load the same mkv into VLC on the same computer and it has the problem.