Remux seems to cause slight pauses

[orionware]

For 5 days now I have been trying to re-encode the movie PI.

I've ripped with SmartRipper and the resulting VOBS playback fine with IFoEdit and WinDVD. I've reencoded the entire movie using ReMpeg2 and TMP with different degrees of bad results.

When remuxed the video pauses for a fraction of a second every once in a while. A quick freeze at random points in playback.

I've created the TMPTemplate per the instructions, messed with variable and constant bitrates and can never get a perfect result after remux.

Is this an issue with IfoEdit or am I missing a crucial step when configuring the re-encode?

I've seen this issue posted before with no real clear cut solution.