Im having troubles with this operation too. After I cut a window (just one) and then I try to do another one it cuts but not to where it has a hole in the fuselage. Here are the steps I take: (NOTE: this is after I have prepared it)
1. Select the boolean operation
2. I select copy
3. A,B
4. Cut. Remove inside
5. then select operand B (or whatever its called)
6. select the box or whatever object I use to make the window.
Thanks for any help