Steps to reproduce:

1. Create new project
2. Add cube to scene
3. Drag it to project tab make prefab out of it
4. Once prefab is created notice that in project tab it has black background instead of dark grey
5. Select prefab and while in inspector, rotate cube shown in preview window
6. Notice that background isn't cleared

Not reproducible: 5.6.0p3, 2017.1.0b4
Reproduced in: 5.6.0p4