Twinmum, I read on the internet somewhere (I'm bad a keeping references, sorry) that in order for stacked stairs to work (normal stairs not the spiral ones) they have to be oriented either North-South or East-West within the world. Again, sorry I can't remember which one. I'm curious to know if you built 2 stacked staircases on one lot, perpendicular to each other, if they would both work?
I just built a house that had this stacked stair glitch and luckily I built it on a square (30x30) corner lot so I just saved it to library and bulldozed the lot and then replaced it with the driveway letting out on the other street and suddenly the stairs work again.
Before rotating the lot, however. I first went into build mode and control-Shift-Clicked on the front of the lot and clicked Set New Front of Lot. That did not fix the stairs so then I went back into build mode and and set the side of the lot as the new front of lot. That also did not fix the stairs but rotating the whole lot did.
This would seem to support Lilygirl's post about the orientation in relation to the world that is important and not the lot it's self.
Man, EA really needs to fix this already.