I'm late, but if this can help somebody, it's time well spent.
If I understand correctly, you want to convert MP4 to FLV using FFMPEG. Here are two command lines to help you do that; I'm currently using them myself (you can adjust them to your needs too) :
ffmpeg -i source.mp4 -c:v libx264 -crf 19 destinationfile.flv
and if the first one doesn't work :
ffmpeg -i source.mp4 -c:v libx264 -ar 22050 -crf 28 destinationfile.flv
Please note that -crf XX
is the quality of the video you will create. It's between 0 and 51 (but between 17 and 23 is a reasonable range and the lower the number is, the better quality the video is going to be).
The -ar 22050
is for adjusting the audio sample range (audio quality). You can choose 11025, 22050 or 44100.
I suggest you read this Tutorial for FFMPEG . It's really complete and has many useful tips.
Hope this will help you or somebody in the same situation.