The kodi.log you've been posted says at line 54 and 55:
This will change when you use advancedsettings.xml to increase the log level.
Line 41 to 50 of your kodi.log quotes your current advancedsettings.xml, so I think it has been loaded fine. If it has no effect on some of your settings, then LE ignores them for whatever reasons.
If you could post another kodi.log at log level 2, then we maybe find answers.