I'm running two PMS from one media folder host on a NAS. I have an old iMac running the latest PMS and the NAS itself (QNAP TS-251C) is running the latest version of PMS.
They both point to the same library/folder but the PMS is not listing some of the TV shows/music and movies correctly. I've sshed onto the plex server and there is nothing of note in the PLex Media Scanner log file (shown below)
Jul 25, 2016 19:28:29.071 [0xf33ffb90] INFO - Plex Media Scanner v1.0.2.2413-7caf41d - debian PC i686 - build: linux-debian-i686 - GMT 01:00
Jul 25, 2016 19:28:29.072 [0xf33ffb90] INFO - Linux version: 3.12.6 (#1 SMP Wed Jun 1 04:53:23 CST 2016), language: C
Jul 25, 2016 19:28:29.072 [0xf33ffb90] INFO - Processor Intel(R) Celeron(R) CPU J1800 @ 2.41GHz
Jul 25, 2016 19:28:29.072 [0xf33ffb90] INFO - /share/CACHEDEV1_DATA/.qpkg/PlexMediaServer/Plex Media Scanner --scan --refresh --section 2
Nothing else comes out of the logs.
I've checked the directories themselves and they are there and correct. Everything looks okay and seems to work okay, but the PMS on the QNAP is missing a large number of TV shows and other files (music and movies)