When we started the Tiger Tube project, we had issues trying to get the AVI files that were generated on the TriCaster to convert over to FLV files correctly. After several hours of research, I came across the following command that converted the file with no issues:
ffmpeg -y -i input_file.avi -ar 22050 -f flv output_file.flv
This is now the main command behind the Admin section of Tiger Tube.