I am not sure if AC9 is still used and hence if any tech support is granted but i have come across a bug in story settings element operations.
If you try to cut a single element from one floor (in my case, a roof) and paste it on some other floor via the story settings window, the whole floor ist cut but only the element you have defined gets pasted to the relevant floor. So you think you have arranged your element but the cost is the whole floor!
Be reminded.
I will check the other versions also for this issue.