To reproduce:

1. Download attached project "904471.zip" and open in Unity
2. In the PlayerSettings, set the D3D Fullscreen Modes to Exclusive Mode.
3. Save the Scene.
4. Build and Run (Target Platform Windows/x86).
5. Click the Windowed checkbox so the app starts up in a window.
6. Click Play! to start.
7. Hover the mouse over the button
Note: Notice that it responds by changing color.
8. Press Alt+Enter to switch to fullscreen mode.
9. Hover the mouse over the button

Expected result: Button responds by changing color
Actual result: Button no longer responds when hovering the mouse on it

Note: Button responds only when mouse is slighty above from the Button
Note: This issue is specific to Windows

Reproduced on Unity 5.6.0b2, 5.6.0b5, 5.6.0p3 and 2017.1.0b2
Not reproduced on Unity 5.6.0b1 and 5.5.3p2
Regression on Unity 5.6.0b2