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Perhaps the roost is not "clearly higher" than the litter. The roost needs to be clearly above what you don't want them roosting on. I can't tell you what "clearly higher" is for your chickens. It may be a few inches and it may be a foot.
Henryetta, I don't believe yours are roosting in the nesting boxes, but that seems to have become a topic.
Chickens are creatures of habit and seem to get stressed at anything new or different. If they roost in the nesting boxes, they will poop in the nesting boxes and you will get dirty eggs. For those that have chickens roosting in nesting boxes, you can solve the problem now before they are laying or you can wait until they are laying, realize you really have a problem, solve the problem, and possibly reduce egg production while they get over the stress caused by the new circumstances. LaSombra is right. The roosts need to be "clearly higher" than the nesting boxes.
The dominant chickens will choose the best roosting spots. If the roosting arrangements change, these chickens will have to determine where they want to roost and this can cause some pecking order issues at bedtime.