One thing I ran into, though it was a while ago, was that disk caching being on would trash performance for writes on removable media for me.
The issue ended up being that the kernel would keep flushing the cache to disk, and while it was doing that none of your transfers are happening. So, it’d end up doubling or more the copy time because the write cache wasn’t actually helping removable drives.
It might be worth remounting without any caching, if it’s on, and seeing if that fixes the mess.
But, as I said, this has been a few years, so that may no longer be actively the case.
I don’t disagree, but if it’s a case where the janky file problem ONLY appears in Jellyfin but not Plex, then, well, jank or not, that’s still Jellyfin doing something weird.
No reason why Jellyfin would decide the French audio track should be played every 3rd episode, or that it should just pick a random subtitle track when Plex isn’t doing it on exactly the same files.