Source File, originally encoded using Quicktime
$ file input.mp4 
input.mp4: ISO Media, MPEG v4 system, version 2
Header:
....ftypmp42....
mp42mp41....moov
...lmvhd.....*..


Output File Encoded in Quicktime,
File:
$ file qt-attempt.mp4 
qt-attempt.mp4: ISO Media, MPEG v4 system, version 2
Header:
....ftypmp42....
mp42mp41..'*moov
...lmvhd......9.

Output File Encoded in ffmpeg:
/usr/local/bin/ffmpeg -i input.mp4 -b 512 -padleft 40 -padright 40 -padtop 32 -padbottom 32 -vcodec mpeg4 -ab 128 -acodec aac  attempt4.mp4
File:
$ file attempt4.mp4 
attempt4.mp4: ISO Media, MPEG v4 system, version 1
Header:
....ftypisom....
mp41....wide..1O
mdat............