There 2 command line sbecause video4fuze connverts the videos using a 2-pass encoding.
Sincerely, i’m not an expert on mencoder, I just made a GUI for it (well, more exactly, it’s a GUI to ewelot’s recommended conversion procedure in linux). I don’t know what mencoder options will solve the volume loss issue (if any), but I think ewelot or people in a mencoder forum or something like that would be more able to answer your question. Once you find the correct options/values for mencoder, you can just put them in both (if not otherwise stated) command lines, and it will work.
If this procedure does not seem easy and straightforward (it isn’t to me, at least), that’s why the command-line editing feature is in the “advanced” menu
Today I noticed this volume loss issue, and I would be happy too to find a solution, but, AFAIK, it’s a mencoder issue, and I have only noted it when converting from youtube flv’s.