Max,
While the presets in Squeeze and Episode are pretty bullteproof, they nonetheless sometimes need tweaking to get better results. Try tinkering with the data rate, frame rate etc and see what you get. File sizes may be a bit bigger but it can make a big difference. Just double click on the preset in the batch window, and make all the changes you want. Your presets will remain untouched, or if you like a setting you can save it.