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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.
This appears to be correct. See:
EncoderAppPath was simply not present at all in encoding.xml! There was only the display value: My own installation was completely fixed by adding /usr/local/bin/ffmpeg
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