In my mixed flock I had 2 SS that were at the bottom of the pecking order. It took me a while to figure it out but they were sleeping in the nesting boxes because a couple of Black Australorps were harassing them whenever they would try to roost.
Once I got rid of the BA's, the SS went back to sleeping on the roosts (and the other girls were happier too).
It might take some time to closely observe what's going on with your flock's dynamics. Maybe some bullying going on?
You could try adding more roosts to see if that would help.