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me too the default ipod profile does not work for me

the mp4 file is not recognized by itunes

Correct commandline:

ffmpeg -i input.avi -acodec libfaac -ab 128kb -vcodec mpeg4 -b 1200kb -mbd 2 -flags +4mv+trell -aic 2 -cmp 2 -subcmp 2 -s 320x240 -title X output.mp4

lastest FFmpeg:

http://surfnet.dl.sourceforge.net/sourceforge/mplayer-win32/FFmpeg-svn-11562.7z