Yes it does,

I guess the problem isn't as widespread as I originally thought. It was Murphy's law that the problem occurred on some of the first movies I converted. The one above is "The Negotiator (1998)". Around Chapter 36 when the computer is shot the sound is off just a little bit and stays that way for the rest of the flick.

But like I said If I play it in QuickTime The delay isn't there.

The Problem is consistent when it happens.