I've updated the links in the first post to to 0.4.0.0 and there should be some significant changes for the better (I hope). Amongst other things the muxing and authoring behaviour has been changed so it should be more compatible with dvd players. Guess it could throw up a load of different trouble though.
Still no ac3 retention, but it shouldn't throw a wobbly anymore when files with ac3 audio are the input.