Ubuntu 16.04.2 LTS PMS Losses Server Setting on Restart

Server Version#: 1.18.2.2029
Player Version#: Web
I recently started having an issue with my server not persisting setting changes like scan for new media frequency and push notifications. Everything else seems to be working fine. Did some searching and this is the closest issue I could find with no solution. I am sure I am not not of disk space (I have run out in the past so that might have triggered something that caused this as I dont remember always having this issue, seems to be newer) and here are my permissions:

drwxr-xr-x 11 plex plex 4096 Nov 18 14:28 .
drwxr-xr-x 3 plex plex 4096 Jul 1 2017
drwxr-xr-x 6 plex plex 4096 Nov 18 13:48 Cache
drwxr-xr-x 5 plex plex 4096 Oct 2 13:29 Codecs
drwxr-xr-x 7 plex plex 4096 Oct 2 13:27 Crash Reports
drwxr-xr-x 2 plex plex 4096 Oct 4 2018 Diagnostics
drwxr-xr-x 3 plex plex 4096 Nov 18 13:51 Logs
drwxr-xr-x 3 plex plex 4096 Jul 7 2017 Media
drwxr-xr-x 6 plex plex 4096 Jun 12 2018 Metadata
-rw-r–r-- 1 plex plex 4 Nov 18 00:28 plexmediaserver.pid
drwxr-xr-x 3 plex plex 4096 Dec 15 2018 Plug-ins
drwxr-xr-x 7 plex plex 4096 Jul 1 2017 Plug-in Support
-rw------- 1 plex plex 985 Nov 18 14:28 Preferences.xml

Grab the log files please (tar.gz of the Logs directory) and attach.

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