hi @omn_ia that variable is defined as false every time you click on the red button. If the app is listed in the conditions of 'CloseThatApp', then it will be set to 'true'. Which cancels out the next 'CloseThatWindow'. If it stays false, 'CloseThat'Window' will be executed. This is also explained at the end of my initial posting 
Look in the conditions of 'CloseThatWindow'. There you'll see the condition that the variable has to be 'false'.
And this is the reason, why I call CTApp before CTWindow. The other way around would make no sense.
Thanks for your feedback on CMD+W. I do not use this. Because of the mentioned problems. The command has the purpose of closing windows, not apps.
F.e. nn the case of Safari, you won't be able to close the open tabs of the last window with this setup.
There are workarounds, but they are complicated. And it is way easier to just press Q instead of W.
And if you are already pressing a combination, I see no purpose in this to be honest.
@hu_hao I guess you should delete all that is related to this setup and reinstall the presets. It should work, like for @omn_ia