When you look around for solutions to this problem, you are usually met with either paid software, or free software bundled with spyware. When all along, there has been ffmpeg, an application that will convert most formats, and is freely available with a big community, and no spyware.
To convert an flv to an mp4, heres what you need to do:
Download the ffmpeg application here:
http://ffmpeg.zeranoe.com/builds/ (pick 32 or 64 bit as required)
For Linux, do:
sudo apt-get install ffmpeg
open terminal, and run command:
ffmpeg -i /pathToInput.flv -f mp4 -s 500x400 -strict -2 pathToOutput.mp4