I have exactly the same problem, same Intel HD Graphics 3000. I believe its connected to this http://forums.introversion.co.uk/viewtopic.php?f=43&t=59325

Just found the update version 3d, also with this update I am still seeing the blocks, instead of trees, while showing the full map. When zooming in most of them go away.

I had the graphics problem on my macbook since I updated to El Capitan. To test currently before updating to the latest build I am running the update 2b- mac os vanilla version from the 16th of december 2015. Showing blocks instead of graphics on the map. With the latest build from the website 3.A (...