What are the permissions on these files/folders? Maybe Jellyfin doesn't have read access?
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I figured it out. For some reason the directories created were owned by root. I did change the ownership of the main directory but forgot that it needs to be changed for the subdirectories as well. In the add folder menu I could see the mounted directory but couldn't access the subdirectories (shows, movies). It's working fine now.
Seconded, its the first thing to check. I am only using local files but depending how I transfer files from other devices it seems they get different permissions assigned. I made it a regular workflow to just run chmod (linux system) over anything new I want to add.
Can you go into the docker container with "exec -it" and try to check if the mount point is mounted correctly and if the files are readable?
Can you list the permissions of the files from within the container? Do you use SELinux?