I don't know if it's still the case as the ffpmeg hall of shame
is offline at the moment, but it looks like Format Factory violates/violated
the GPL license at some point - as many of these "free" video encoders are wont to do.
What happens is people get ffmpeg and the various other free encoding tools that people work their asses off on, wrap a basic GUI around it to do common tasks, then put ads all over it and make money off their hard work, while not complying with the terms of the ffmpeg licensing. Often this is just ignorance and/or laziness rather than outright malice, but it's still lame and people should be aware of problems with their software!
So you should use Handbrake. Also Handbrake is probably better anyway.