That's what happened; they no longer sleep in the boxes. I have caught my Silver Lace Polish girl sleeping in the boxes a couple of times but I think it's because the bigger girls pull her feathers so much she just moves.
I am having the same problems; I have 7 hens and each next box has a perch in front of it. All 7 hens want to fly up to the perch in front of the highest boxes and sleep. So I am guessing from all the posts that the boxes need to be lower than the roost and enclosed.