The rip now produces a Users\Lindsey\MakeMKV_log.txt file on 3800Client, a Vista (64-bit) computer, after I woke up and changed the MakeMKV preferences to require it. The log file is the first attachment.
I am now on v 1.6.0. The rip produced 12 output title files and as far as I can tell this is everything on the disc, including the main movie file. I played each title file on MediaClient (Win 7 64-bit) using VLC 1.1.4. Those title files that I thought would include audio tracks did produce sound. A snip of the directory \\MediaServer\MyMovies\HD-DVD MKVs\Dune\ is the second attachment.