I use media player classic and WMP to play the clips but i have just tried VLC player (Which i normally only use for FLV movies), and i get the same issue too. I will look into it and see if i can fix.
Cool. VLC do have a public bugtracker but they don't seem to be very active at using it in my experience, although my stuff has been more transcoding-based instead of playback so it might be worth a shot if you can't solve it at your end.