Interesting, I thought it was happening for all MPEGs but you may indeed be correct there.
Edit: Nope, I just converted an MPEG-1, and lost the sound.
I'm wrong.
Just imported an mpeg-1 video into iTunes then converted it and lost the sound.
I figured it out.
Follow these simple steps :
Open the mpeg-1 movie with Quicktime
Export it as Movie to hinted movie.
Select options and then make movie self contained and mpeg muxed.
It winds up a QT movie of the same size and is converted pretty fast.