Its not really a bug, but there is more than one place where you can set the cut plane.
if you have a "view maps" set up with different layer settings then you will need to update the Cut-plane interface box for those layer settings along with the universal cut-plane interface.
Try looking at the uncut line pen aswell.
As for the stairs, select "story sensitive" and turn it on, you'll then get an additional dialog line "2d above home storey" you cna turn numbering off in there.
Hope this helps