{L_BUTTON_AT}haborg
For anyone who hasn't yet talked to the Support Team: when I upgraded to TOS 5.1x, I noticed two changes. First, the main folder is renamed to Volume1 (or Volume2, 3, or however many volumes you specified). The old /mnt/md0 (or 1, 2, ...) filepath snippet is obsolete. If Plex is storing that, you need to change the listing in all libraries.
Second, you have to grant Read/Write permissions manually on the /public folder and to the Media User Group on that same folder. See Control Panel -> User Groups for details. Select Media User Group and then click Edit, and then select Permissions. The /public and /Plex folders should both have Read/Write permissions granted to this group. Until they do, Plex can't even see the library folders.