Press a hotkey to make the current window transparent, allowing you to see through it! Press hotkeys to minimize/maximize the current window, or to send it to another monitor (like Windows 7, except also if you don't have Windows 7)
Make a window transparent while 'make window click-through' is checked
Uncheck 'make window click-through'
Click the window and notice that it still clicks through.
Effectively, this bug makes it to where you can never get back to your window. If the window in question cannot be alt-tabbed to (often applications have secondary windows they create), you will never be able to recover focus on this window, because of this bug. However, the 'keep on top of other windows' feature is correctly removed when unchecking the check box, and so as you click through the window, the application receiving the click-through is now made active and your window moves behind it.
Steps to reproduce:
Effectively, this bug makes it to where you can never get back to your window. If the window in question cannot be alt-tabbed to (often applications have secondary windows they create), you will never be able to recover focus on this window, because of this bug. However, the 'keep on top of other windows' feature is correctly removed when unchecking the check box, and so as you click through the window, the application receiving the click-through is now made active and your window moves behind it.