Mother cats have an instinct to move their kittens from time to time to avoid predators. Domestic cats won't do it as much, but if the box was in a place where she thought there was any kind of danger - too much human traffic, noise, light, she would decide to take them somewhere she thinks is safer. Even if it's really not. Look at the box and think of her feelings - what would you not like about it if you were her protecting her babies, and then maybe you can make the right adjustments and get her back into it. sometimes putting the box into a half open closet makes momcats feel more secure.