Steps to reproduce:

1. Open Unity;
2. Open attached "Main.unity' scene;
3. Enter Play mode;
4. Observe the Rendering tab in the Profiler window;

5. Notice that instancing works correctly - most of draw calls are batched together;
6. Stop the scene;
7. Drag 'main2.unity' scene to the Hierarchy panel;
8. Select 'Main.unity' scene in the Hierarchy panel;
9. Enter Play mode;
10. Observe the Rendering tab in the Profiler window and the scene rendering in Scene/Game view.

Actual result:
- Non-instanced draw calls are increased (from 50 to 9000) along with the instanced ones (from 5000 to 20000).
- Scene rendering is broken - spawned rocks are much brighter than in the initial scene.

See attached gif video and actual.png screenshot.

Expected result:
Performance and scene rendering should stay the same with multiple scenes in the Hierarchy tab (see attached expected.png).

Workaround is to unload scene in the Hierarchy by right click on it --> Unload Scene.

Notes:
- Reproduced on Windows 10 for Unity 5.4.0a6 and 5.4.0b1.