To reproduce:

1. In a new project, create a script
2. Go to Edit -> Project Settings -> Script Execution Order
3. Drag a script to the custom order
4. Select any other object in the scene to close the Script Execution Order window
5. Observe the absence of pop up dialog

Expected: closing the Script Execution Order without saving shows the pop up dialog
Actual: pop up dialog to Apply or Revert changes is not shown when closing Script Execution Order without saving

Reproduced in 2017.1.0a1, 2017.1.0a2, 2017.1.0b1, 2017.1.0b6, 2017.2.0a1
Did not reproduce in 5.5.3p2, 5.6.1p1
Regression introduce in 2017.1.0a1

Fixed in 2017.2.0a2