I've had invisible-brush-trouble with a decompile of Niveus, and sometimes even deleting the wrong brush and copying a similar but working brush from somewhere else to that place did not fix the problem. But then I tried clipping, and that worked. To clip a brush seems to remake it completely in its new shape. That's something you could try. Drag the brush bigger, then clip it smaller again.
You could also check if the brushes (vertexes) are perfectly aligned. Don't move them, that does totally fail in my experience with NetRadiant. Those things always have to be fixed via clipping.
And I've had a shadow problem once, too. I had a glass box directly at a wall, and a small portion of the wall had a shadow. I moved the box away from the wall a few WU. Doesn't apply here, though.