SOLVED: Playback issues after update

[Despair]

In the Portainer page for Jellyfin are there any environment variables that would change the ffmpeg path?

No, seems good to me:
   

It matches screenshot from theguymadmax

[TheDreadPirate]

Let's try this. Stop the Jellyfin container and back up /config. We aren't going to touch it, but better to be safe.

Once you've backed up /config I want to prune all the VFS and images currently not being used. I don't know if there is an equivalent in the Portainer UI, but you should be able to run this on the command line.

Code:

sudo docker system prune -a

Once that completes, start up Jellyfin.

[Despair]

Let's try this.  Stop the Jellyfin container and back up /config.  We aren't going to touch it, but better to be safe.

Once you've backed up /config I want to prune all the VFS and images currently not being used.  I don't know if there is an equivalent in the Portainer UI, but you should be able to run this on the command line.

Code:

sudo docker system prune -a

Once that completes, start up Jellyfin.

You can delete unused images and volumes inside Portainer, but it's not the same as the command you posted because that one said it was also going to remove stopped containers, it's more aggressive.
I have old volumes with data I want to backup, so I didn't confirm your command and only tried to delete unused data from Portainer, and then I restarted Jellyfin. By looking at the startup log I found this:

   

For some reason, the wrong ffmpeg path was declared inside the entrypoint. I deleted that part and now it works!