Alan. If you are using macports, my apologies. If you are not, just download macports and follow the instructions here to build ffmpeg.
http://ffmpeg.darwinports.com/
Also, the newer version of ClipGrab has a newer version of ffmpeg with the dreaded "non monotone timestamp ffmpeg >=" error.
For many files this will prevent the rewrapping. Just paste the ffmpeg portion of the script to the terminal (if you find this workflow to not work) and you will see this error.
One option it to extract the version of ffmpeg that works (I cannot find the older version of ClipGrab that I used).
Another version is to use VLC for decoding and ffmpeg for encoding. I could not find an option for this.