Help with subtracting

Any info would be a great help.

I was working on my map last night which is coming along well, when I ran into a new problem with subtracting. I have a completed room that I would like to add a new room off of. The new room will be connected via a window. I made a cube the size I wanted the window to be and subtracted it from my room, it worked fine. I then porceeded to build a cube the size of the new room. I lined up the cube with the back of my window, which is about 20 pixels deep, and hit sutract. Instead of my room being added and removing the back part off the window, my room was added and it remove majior parts of the existing walls, ceiling and floors of the existing room and rooms below it. The new cube does not come into contact with any other brushes other then the window, but it still removed parts of other brushes. I tried building the new room in a remote area, which worked fine, however as soon as I relocated the new room to the back of the window and rebuilt the geomotry, the same thing happened, walls, ceilings and floors dissappered. I have many other rooms built the same way without this problem.

Any ideas???