Workaround solutions for this are launching in windowed mode or clicking the Arma 3 logo on start up when it's loading addons and that stuff. Just need to be careful with the "Arma 3 is not responding" pop-ups that are caused by the clicking because you can quickly accidentally click the close program button. That's why it's likely some kind of a windows focus issue.
EDIT:
Launching windowed is the only workaround.