The issue has been happening all day, anywhere from every hour to every 30 minutes. Turning on Silent Mode does nothing. In fact, right-clicking the tile icon and checking Silent Mode has the app like normal, when unchecking it puts it in Silent.
Update 23 Sep 08:55 EST:
Before bed, locked my computer. When I woke up, computer was at the screen to enter my password to unlock. Unlocked my computer, and the app was already open. Don't know if that means anything, but thought it should be noted for the sake of bug-logging.
Minimizing doesn't fix the problem, the GUI will eventually pop up again. Might have found a temporary fix; open the GUI, click on Menu in the top-right corner, then minimize. I've gone a couple hours without GUI popup so far.
Update 23 Sep 14:53 EST:
Three popups in 6 hours. Don't know if the experiment listed above had anything to do with it.