I duplicated this today, encoding an MPEG-4 file with x264 resulted in a
warning from MPlayer:

warning: first frame is no keyframe

This was after carefully using the key frame seek buttons in avidemux to
find key frames to cut on. The first few frames of the video are missing
colour information. vlc makes a better job of playing the video clip and
doesn't complain, but there is still some distortion visible in the
first few frames. So I do think this is a bug in avidemux or x264.

-- 
avidemux, there are no keyframes during recoding a video
https://bugs.launchpad.net/bugs/331345
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