This whole setup seems a little unstable to me.
Talk to the ffmpegx folks about having a GUI front-end over a command-line backend. It doesn't seem to bother them.
Indeed, I submit that a GUI (or web) front-end over a command-line backend is actually more stable, since you have a very, very clean interface between GUI and command. The command can evolve at a different pace from the web, as long as the command-line options are compatible, you have no possibility of breakage.