It's interesting that this was never a problem until recently. I've seen people say that about stacked stairs and the orientation of the lot before but I was never able to reproduce the problem they spoke of before and I use stacked stairs in almost all of my builds. It is,after all, how they are often placed in real buildings. It just makes sense to stack them. These aren't even new builds I've been having problems with but a few of my oldest favorite residential builds that I've used many times but some how recently they stopped working.
Anyway, I found a solution mentioned on another site that was much easier then redesigning the whole floor plan in a way to rotate them 90 degrees. I just slid the upper stairway back by one square so they aren't directly over top of each other. This only eats up one square of floor space so it was relatively easy to do and now they work fine.
Yet another bug on the long list of bugs EA will never fix I guess.