Server Version#: DS415+ @ DSM 6.2.4-25556, Plex v1.22.1.4275-48e10484b
Out of the blue, my PMS stopped displaying new media files.
While reviewing the Plex Media Server.log, I found many, many instances of “Failed to add watch for…” followed by the path to one of many, many folders under my media directory.
I looked in the Syno interface to make sure the perms were correct - yep, the Plex user had RO perms to the entire tree.
Rebooted, looked at the logs again, same error.
Found a similar problem with an answer by @ChuckPa and tried his fix. Restarted PMS. No more errors. All files visible.
Thanks, Chuck 
find /volume11/Videos -type d -exec chmod 755 {} \;
find /volume11/Videos -type f -exec chmod 644 {} \;