But that seems unlikely… at best a coincidence… or there is some other method being called that is modifying the main scene graph.
The error indicates that some child of rootNode has been modified outside of the normal update pass. Either because you are modifying things from your network listeners or maybe because you are modifying them from your GUI controller and it happens at the wrong time somehow (very strange if so).
When I see code like the above, my first instinct is to blame it on network message listeners since the messages come on a different thread and the listeners must never ever ever do anything directly with the scene graph.