I just read you post and tried creating a box and then subtracting a cylinder from it. No problem, worked great. Then I tried to bevel the edge of the circle and got the same results as you described. I found a way around it for me and I hope it works for everyone else too.

Before you perform the Boolean difference, use the split polygon tool to draw a line accross the cube but make sure the line goes through part of the cylinder. Now perform the boolean and then bevel you hole. It worked for me every single time (as long as there was one line (edge) going through part of the cylinder.

Hope this works for everyone.