I had this issue, and I just kept painting and it fixed itself. Sorry if that doesn’t help. I’ll load up the project I did it on and see if I can get it to happen again.
Edit: Once you start painting, it should start compiling shaders. After the shaders compile mine stop taking up entire squares. You may need to put down a base layer first, then try painting on top of the base layer.
edit 2: yeah, you’ll need to paint one on as the base layer first then paint on top of it. http://puu.sh/82fLH/8137ed0e1f.jpg
