Command line notes
stream copy from mp4 to flv
Copy from mp4 container to flv container at 30 frames per second.
ffmpeg -i input.mp4 -acodec copy -r 30 -vcodec copy -f flv output.flv
encode to .mp4 with h264 and deinterlace
This seems to work the resulting file plays in Quicktime, but doesn't play in jwplayer so probably still needs more tweaking.
ffmpeg.exe -i input.avi -ab 256kb -vcodec libx264 -b 1000kb -deinterlace output.mp4