Is it related to this issue posted to the bsd forks github?
I cant help you directly as I run Jellyfin on linux, but that should be your first port of call.
just keep in mind jellyfin on FreeBSD is 100% unofficial so you are on your own.
EncoderAppPath was simply not present at all in encoding.xml! There was only the display value: <EncoderAppPathDisplay /> My own installation was completely fixed by adding <EncoderAppPath>/usr/local/bin/ffmpeg</EncoderAppPath>