Do you have any ".ignore" files anywhere in your library? Can you open a shell for the container and navigate and see the files in the container shell?
Jellyfin 10.10.7 (Docker)
Ubuntu 24.04.2 LTS w/HWE
Intel i3 12100
Intel Arc A380
OS drive - SK Hynix P41 1TB
Storage
4x WD Red Pro 6TB CMR in RAIDZ1