For what it's worth, the bug and fix that are linked by bubba also worked for our 10.3 web adaptor.
Our symptom was that when we would access http://localhost/arcgis/webadaptor in order to configure it to one of our sites, we would get the error listed above. With the exception that our web adaptor is installed in a different directory on \\D.
Once full permissions were assigned to the ArcGISWebAdaptorAppPool user to the config file within the web adaptor folder no problems were reported .