Converted a dozen or so 20-30 minute videos. First 2-3 play fine all teh way through with no problems. Most of the rest will 'pause' the video for 10-15 seconds while the audio keps playing without a hitch. The video will them skip ahead to catch up play 1-2 frames then pause again.
All video's are from the same source (First season on Mind of Mencia). Re-encoded them all at the same time with the same settings with the software linked in post #1.