Just an update as it seems to be causing some confusion...
To use the debian init.d script I posted previously, you need to modify the PMS.sh file
Because the init daemon has no working dir, you have to make sure it is working in the pms installation dir before it runs up the java. The java code expects the .conf files to be in the same working dir when it starts up.
So, the last 2 lines of the PMS.sh script have to look like this:
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exec "$JAVA" $JAVA_OPTS -Xmx768M -Djava.encoding=UTF-8 -Djava.net.preferIPv4Stack=true -classpath "$PMS_JARS" net.pms.PMS "$@"
Note there is NO AMPERSAND on the end of the exec line, because that breaks the pidfile mechanism in the init script.
If you get this wrong, it will probably start up ok, but since it fails to load the pms.conf file ('cos it can't find it) you will find the path configuration is ignored and the PS3 will show the whole dir tree of your server, all the way from root.
And lastly, if you use a separate user/group for the pms daemon, remember to set the permissions up so it can read the conf files, execute the PMS.sh script, write to the database AND read your media directories...
The easiest way to test this is with "su ..." and then trying to access/execute the relevant item.
So endeth the lesson. All hail PS3 Media Server.