Plagiarizing myself from a post yesterday…
By default, because of the ACLs associated with it, only your user can access files under /media/pi. This is due to the way the disk is automatically mounted. The recommended way to use extra disks with Plex Media Server is to create static mount points and the necessary entries to mount them there in /etc/fstab. That method is described in @ChuckPa’s Linux Tips post:
There are ways to modify the default ACLs associated with the auto-mount location, if you’re interested in trying that instead. In your case, the command would be:
sudo setfacl -m u:plex:rx /media/thomas
This gives plex
read and execute permissions to that directory. Assuming the permissions on the files and directories beneath are suitable, this will give PMS all the rights it needs to see your media.