Handbrake (loaded from “muon discover”) crashes if you try to put in a source file.
When using netrunner Enigma II it works fine. It may be a different version.
This applies to mp4 and flv files that I tested.
I was able to use Handbrake on my Enigma II to process the files on my Netrunner 14 system (same computer).
the version that crashes is : HandBrake rev5474 (x86_64)

Can you start it from the command line and report the possible error message appearing after the crash ?