I was trying to convert xvid avi to mp4 by keeping the vocdec with copy and acodec with libfaac. My vid's frame rate is 23.98.
There is a warning when then encode/mux begins
Seems stream 0 codec frame rate differs from container frame rate: 23.98 (65535/2733) -> 23.98 (10000000/417083)
Unfortunately even when I try to use force by -r 23.98 or 24000/1001 or 24 before the -i input file, its not having any effect. I tried with higher 25, same warning was present, with the bad public atom error in qt and same frame rate 23.98.
Seems like it might be a 64-bit timescale bug, My ver of ffmpeg is FFmpeg svn rev 14277 - 07/18/2008 from http://oss.netfarm.it/mplayer-win32.php