I have only a few scenes in a new model, 2- hours in so far. (preparing for producing architectural floor plans, so each scene has different layers on/off).
When I update one scene, others are updating and end up looking the same- more than one, but not all. I tried updating scenes using both ways- update the tab and also update in the scene window (where you are prompted for the properties). both ways seem to have the same effect. More than one scene gets updated. I turn a layer off, update the scene, then see the other scene updates and looks exactly the same- that same layer is off.
i just updated to the latest 2016 version today. 16.1.2418.