Where is your media stored on the Synology NAS?
When you install Plex Media Server on a Synology NAS running DSM 6, the installation process creates a /Plex shared folder.
That folder is reserved for use by Plex Media Server. You must not place any media in that folder, otherwise Plex Media Server on the Synology NAS may (will) fail to function correctly (it is OK to use /Plex if the NAS is running DSM 7)
If you have media in that folder, you must move it to another location.
See Installation & Setup of Plex Media Server on Synology and Synology FAQ (DSM 5 & 6) - Questions, Answers, and a few How-To’s for additional details.