I've never used Lives before, but the steps from the guide to convert video files from one format to another does work. I use it to convert some mov, avi, wmv files into mpeg1 and mpeg2 formats and I get both audio and video.
You can try these.
mencoder -of mpeg -ovc lavc -lavcopts vcodec=mpeg1video -oac mp3lame filename.mov -o filename.mpg
This syntax is similar to the first one I gave you, the only change is the -oac copy to -oac mp3lame. This will convert the audio in the mov file to mp3 format.
If you have ffmpeg installed, try any of these
ffmpeg -i filename.mov -target ntsc-vcd filename.mpeg
ffmpeg -i filename.mov -target ntsc-svcd filename.mpeg
ffmpeg -i filename.mov -target ntsc-dvd filename.mpeg
The ffmpeg command will convert the mov file to a vcd/svcd or dvd compatible MPEG1 or MPEG2 format respectively. If your country uses PAL, subsitute ntsc with pal like so, pal-dvd.
if no luck, try these suggestions
If lives can open avi files, then convert the mov file to an mpeg4 avi file
mencoder filename.mov -ovc lavc -lavcopts vcodec=mpeg4 -oac mp3lame -o filename.avi
Then use lives to convert the avi file to mpeg
if unsuccessful, are you runnung the latest versions of mplayer and Lives?
Do you have the latest codecs? As of this post, the lastest codecs for mplayer is Linux x86 20071007
Use your package manager and upadte the database, then search for mplayer and Lives. Your package manaager will tell you if any upgrades are available.
Visit the Lives website. Search for any forums, knownledge base and or support area where you can search or submit a problem. You can also submit a bug report informing them that Lives can preview a mov file with both audio and video, but during the encoding process, no audio is present. If there is no help on the website, you can download the tarball of Lives and search for the email address of the maintainer of the program. Sometimes they welcome bug reports for their programs.
Let's hope this helps.