I had a very similar issue where my plex server was running perfectly, but i couldn't stop the service. I would also get "plexmediaserver not running? (check /var/run/plex/plex.pid)." It also showed in the freenas GUI as being turned off even though everything was working fine.
I remember messing with permissions a few days ago by making plex run as media:media. I forgot that might mess things up. So to fix the problem, I just needed to change the permissions on the plex directory: "chown -R media:media /var/run/plex". I also changed the owner of the fcgi file too. Once i did that, I stopped the jail and turned it back on and now everything is working normally. My freenas GUI says its turned on and now I can stop and start the service via putty.
I hope it helps someone who is google searching.
in: /var/run/
old:
drwxr-xr-x 2 plex wheel 2 Dec 10 09:14 plex
-rw-rw-rw- 1 root wheel 5 Dec 10 09:14 plexmediaserver_fcgi_server.pid
new:
drwxr-xr-x 2 media media 2 Dec 10 09:14 plex
-rw-rw-rw- 1 media media 5 Dec 10 09:14 plexmediaserver_fcgi_server.pid
I have same exact problem here, my plexmediaserver won't start (I'm getting "some error occurred" when starting the mediaserver)
The following command didn't work for me either..
"chown -R media:media /var/run/plex".
"chown -R media:media /var/run/plexmediaserver_fcgi_server.pid".