I see that picture # 1 is the before and picture # 3 is the after of the nest walls. It looks like there is only an inch or two of triangular space, not enough for a chicken to try to roost upon. Good!
Now the roosts. I believe that is your problem. As
@aart said, they don't look comfortable. The ladder is a steep angle not allowing room to fly up to easily or stand up as the rung above them is in the way and has another chicken on it which will poop on the one below it. I can't really see the other roost well but I think it goes along the side wall. How far from the wall is it? It needs to be a foot away. You could add another on the opposite wall, again 1 foot away from the wall, also at least 1 foot between the roosts. Considering the size of the coop there might not be much room to be able to fly up to the roosts. Can they be placed 1 foot above the floor?
Now, the coop size. 5x7 does accomadate 8-9 chickens. Do the nests sit on the floor? If so their dimensions must be subtracted from the floor space. Example: 3 nests 1sqft each means you have lost 3sqft from the coop living space. You're now down to accommodating 5-6 chickens. Your top six chickens have claimed the prime roosts. Your other 3 are not naughty, they are simply at the bottom of the pecking order. One way to remedy this could be to rebuild the nests on the outside of the coop freeing up that space and probably making it easier to make comfortable roosts and take out ladders.
I hope you can work this out. Your girls are all so pretty I'd never be able to get rid of any!