I have two of the one with the staircase. I love it.

There could be a lot of reasons for it and she may just need to be retrained entirely. Treat her like a kitten and rub her paws through the litter every time she starts to go out of the box, that sort of thing. It could also be the type of litter you're using and all the changing of boxes. Cats are creatures of habit and she may feel overwhelmed.

One other reason could be she is having trouble pooping or has had such pain from it in the past, now she is trying to control it. Cats can associate the sound of the urine or poop hitting the litter with the pain and therefore do whatever is necessary to avoid that. It could be something as simple as worms (which you may not even be able to see) or something more complex.

Either way, the best thing you can do is try to stay calm because your stress will influence her stress levels and likely make the problem worse.