movies with high-contrast and color that have fast moving scenes are really the only ones that would be affected by being compressed too much as far as I have found. Done about 90 so far. The commentary issue definitely sounds like something happened in the audio selection area of the compression tab. Sometimes the streams are not labled as to what they are, just "AC3-2ch" AC3-5.1ch"....etc. Unless you know for sure what the streams are you're taking out or mesing with, I wouldnt even bother unless the stream is over like 500megs.
PULP (pulp) n. 1. A soft, moist, shapeless mass or matter. 2. A magazine or book containing lurid subject matter and being characteristically printed on rough, unfinished paper.