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:
- Change the username Plex runs as
- 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 -