Is it an imported glass? Make sure that solid when bolean rendering is checked. It's right under the smooth unsmooth part of the edit window. Sometimes how objects intersect affect how this works. Try shifting the rock just a bit. The short explination is you have to have an odd number (3) of points to draw a triangle for your mesh. If you only have 2 points intersecting that surface will not be created. By playing around with how the rock intersects sometimes you can overcome this by chance.