Plex will not find videos within the folder that I associate with a library

This is normal Linux-Gnome behavior when the automounter is mounting USB or NTFS drives under /media/<username>. Nothing will be visible to user plex.

Your options are:

  1. Change the username Plex runs as
  2. Change the mount point (make an entry in /etc/fstab)

To change the username Plex runs as, see here -

To gain control of the USB / NTFS drives and how they mount, see here -