In QuickTime Player 7.5 (and various other QuickTime framework-using programs, though not all), exporting a file decoded by Perian 1.1 that contains MP3 audio (.avi and .flv containers tested) results in a file with a silent audio track.
Here is a sample .avi file with MPEG-4 video and MP3 audio:
http://homepage.mac.com/tylerl82/test.avi
Steps in QuickTime Player (Pro required):
File -> Export...
Export format: "Sound to Wave" is the quickest, though "Movie to MPEG-4" and "Movie to QuickTime Movie" also demonstrate the same problem.
The resulting file will have a fully-formed audio track, though it will be silent.
The same original file saved/flattened as a QuickTime .mov reacts identically, though strangely enough, iTunes will convert the .mov version with full sound.