I have been trying to transcode a quicktime movie file to an flv format 
using
  
  $ ffmpeg -i Demo_FlagOfOurFathers.mov Demo_FlagOfOurFathers.flv
  
.

The file is a 7 second movie according to the binary reading of the
file. I used http://developer.apple.com/documentation/QuickTime/QTFF/qtff.pdf to        read the binary file. Apple's quicktime player also recognises the file as 
a 7 second movie.

This file seems to have one video stream, one audio stream and one data 
stream.

The length of the video stream is 11 seconds but the frames in the first four           seconds are not to be transcoded nor to be displayed. I suppose that they exist         just for the referencing purpose. That is, even if the length of the video
stream is 11 seconds, the frames are to be laid between the timestamp -4
sec and the timestamp 7 sec, and the frames between the timestamp -4 and the
timestamp 0 are not to be transcoded.

The length of the audio stream is 7 seconds.

However, FFmpeg is not aware of this, recognises the movie as an 11
second movie, and transcodes every frame. Consequently, the transcoded 
movie has extra frames visible at the beginning of the movie and its a/v 
sync becomes awkward.