I was all prepared to get all into ugly troubleshooting territory with Plex, which has a transcoding failure every time I've tried to play something lately. I tried rebooting the Pi that it runs on last time and still got them.
So, I thought it was some kind of permissions thing and was looking at seeing if it was really using the transcode directory I set it to use, I was also prepared for the ugly truth that some Plex update made it so that a low-power computer like this wouldn't be able to transcode as well and started looking at mini PCs.
It just started working again. Why? I have no idea. There was an additional reboot between the last time it didn't work and now. Maybe the new rule should be always double reboot.