How to get Jellyfin to see files in a media library?

Jellyfin can find my media files if they are within a subfolder of my media like \shows\Show1 but if I have any loose media in \shows\ it just doesn't scan them properly. I can find the em in the "Episodes" tab of the library but it doesn't seem to show them in main library tab. This affects using android/fire tv apps that browse the folder as they only show what's in the main listing.