Application becomes completely unclickable/uninteractable sometimes
Personally, I have encountered similar behavior with applications when Windows fails to display a pop-up dialog. That is, either the application itself generates a general pop-up, which is hidden by the main UI window, or generates a Windows UAC prompt that is otherwise hidden for some reason.
I might suggest using Alt + Tab to cycle through open desktop windows the next time this occurs, to see if either of these situations apply. If so, closing or cancelling the pop-up should (ideally) help to resolve this issue (i.e. make the main application window responsive again).