Apple Compressor and bad audio fades: solved.
 

If you happen to have the fortune of using Apple Compressor to prepare video+audio uploads for YouTube and have ever wondered why your audio fades were not working: the bug seems to relate to the way the app passes the audio data to the codec. You can fix this by using linear PCM. Doesn't make much of a difference in the file size and YouTube will recompress your audio to AAC anyway.