Steps to reproduce:
1. Open the attached project (FullScreenTestProject.zip)
2. Open the Assets/Scene.unity scene
3. Run and build
4. Play the Game window on a main screen(windowed mode)
5. Move the Game window to a secondary screen (with auto-resizing)
6. Press alt+enter (enter full screen)
7. Press alt+enter (exit full screen)
8. Observe, the Game window will appear on the main screen

Expected result: Game window should appear on the same screen
Actual result: Game window appear on the main screen

Reproduced with: 5.4.5p1, 5.5.2p4, 5.6.0f2, 2017.1.0a5

Fixed in:
2017.1.0b2