aHA! Thanks for posting the macro and the video. I know exactly what you're talking about now. Unfortunately I don't have an answer for it. I experienced the same issue back in august and brought it up in two different topics.
Prompt for User Input Window Not Appearing Even Though It Is Triggered
Possible Bug: Manipulate a Window Interacts Differently (And Unreliably) With Different Applications
I believe that in my case it had to do with another window management application I was using at the time, which I stopped using. I no longer have the issue. Do you use any other window management software, like Magnet, Rectangle or the like?