For me it's not black boxes, but horrible fragmentation of the graphics on some maps, mainly the urban ones. Example. I think it has something to do with multi-story buildings. The fragments will change depending on what is illuminated/moused-over, and such. Sometimes the fragments are extreme-zoomed in portions of my xenonauts.
I'm using the latest version from the Humble store, 1.0 31/05/2014, on a 2010 MacBook Pro, OS 10.8.5