Such as? I do not know what would interfere like this.
i used to have disable programs such as razer synapse, because the notification for updates would minimize whatever i was doing. when that happens, try to look in your hidden icons and see if something new is opened. if nothing like that happens, then its possible it is just the game being stupid. other than that i would not know how to help without having access to your computer, because i do not know what kind of programs you have.