did you try Arsta or Transmageddon?
I recommend distributing a recent ffmpeg (from FFmpeg) binary with the GUI. This way you can only have to deal with one version (not to mention any forks). Otherwise you're going to be spending too much time trying to support everything. Recent ffmpeg builds are already available if you don't want to make it yourself.
Or you can use the FFmpeg API if you prefer (I have no experience with this but see "docs/examples" in the ffmpeg source for a start).
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