Andrew Heard <[email protected]> added the comment:

Thanks for looking into this. I have submitted a zip file containing the 
original Apple Lossless file created using afconvert as Sample 
CoreAudio.m4a (this is the one that works with iTunes sharing) and the 
file Sample FFmpeg.m4a created with FFmpeg.

The command I used to do the conversion and its output was:

ffmpeg -i /Users/andrew/Desktop/Sample\ CoreAudio.m4a -acodec copy 
/Users/andrew/Desktop/Sample\ ffmpeg.m4a 
FFmpeg version 0.5.3, Copyright (c) 2000-2009 Fabrice Bellard, et al.
  configuration: --arch=x86_64 --enable-static --disable-shared
  libavutil     49.15. 0 / 49.15. 0
  libavcodec    52.20. 1 / 52.20. 1
  libavformat   52.31. 0 / 52.31. 0
  libavdevice   52. 1. 0 / 52. 1. 0
  built on Feb 17 2011 08:12:38, gcc: 4.2.1 (Apple Inc. build 5666) (dot 
3)
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/Users/andrew/Desktop/Sample 
CoreAudio.m4a':
  Duration: 00:00:11.12, start: 0.000000, bitrate: 729 kb/s
    Stream #0.0(eng): Audio: alac, 44100 Hz, stereo, s16
Output #0, ipod, to '/Users/andrew/Desktop/Sample ffmpeg.m4a':
    Stream #0.0(eng): Audio: alac, 44100 Hz, stereo, s16
Stream mapping:
  Stream #0.0 -> #0.0
Press [q] to stop encoding
size=     988kB time=11.15 bitrate= 726.3kbits/s    
video:0kB audio:987kB global headers:0kB muxing overhead 0.163319%
File 'Sample alac files.zip' not attached - you can download it from 
https://roundup.ffmpeg.org/file1365.

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