Someone correct me if I'm wrong, but certain .mpeg video clips have muxxed audio/video. For these to be properly converted, you need to demux the audio and video.
Several utilities to try, besides the one built-in to Quicktime, are:
ffmpegX
HandBrake
iSquint
MPEG Streamclip
I'm sure others have their favorites. But so far, with ffmpegX, I have been able to properly convert any video file to an iPod-friendly format (with the exception of certain Windows Media File clips).