Why are you demuxing with something other than eac3to? My process is to put HD-DVd in drive with AnyDVD running, point top it with eac3to, get the track listing, then pull the desired video out to a MKV and grab the desired audio to an AC3. Compress with meGUI using x264, merge with MKVmerge, done. 20+ movies and I've had zero issues with the output. Only weird one was the first Harry Potter, still not figured that one out.
http://forum.doom9.org/showthread.php?t=135361