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Thanks for the ideas.
GPU does seem to be passed onto the docker container, not only because of the dramatic increase in speed, but also because the CPU isn't being maxed out like it was before adding the GPU hardware line.
Volumes are bind mounts.
I experimented with permissions and user groups, and noticed no difference to the behaviour in render output.
For these videos, quality isn't super important, but file size is. I spent most of yesterday tweaking settings on my local Handbrake install to get the right balance. So, I assumed transferring the settings over would give the same results.
Are you running different versions of the software? (e.g. different versions of ffmpeg, maybe?)
Same version of Handbrake (1.9.2), but I'm not even sure how to check for the ffmpeg version on my NAS, or what Handbrake is using. The system panel in the Handbrake info window doesn't list ffmpeg at all.