I think this kind of blinking happens because the given application needs your attention. I tend to think this is a Windows thing, not an ARCHICAD thing.
If I start ARCHICAD, then immediately switch to a browser, then ARCHICAD will load in the background and then start blinking in the Taskbar. If I switch to it I can see that it displays the Dialog with the licence information which I need to click to proceed.
I do not find anything wrong with that.
I think other applications will blink as well when they need your attention or input.
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