Confirm on the black boxes.
In my case, they appear on random missions. Save / reload mid mission doesn't help, only reload of a pre mission save does. The boxes seem to mostly cover moving stuff like smoke, moving alien animations etc., which sometimes even triggers it. It isn't as if the game couldn't load the animation, because sometimetimes they randomly appear again only to vanish again. The main problem is though, even though the game remains playable otherwise, sometimes when the camera looks at an area which is obscured by these black boxes in a large part, the framerate drops to unplayable levels. I am talking about 60 fps to 0.2 fps drops. When I try to exit the mission (Return to main menu) or reload right then, the game crashes. The reloads are only possible after restarting the game.
Let me know if you want a crash report or a video of the problem or something. It makes the game pretty much unplayable as it occurs in about every second encounter.
I am on 2012 MBA (Intel HD4000) with Mavericks on it, playing the latest Humble store 1.0 31/5/2014 build.
