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This is a picture of it I found on google.
http://www.mitzenmacher.net/blog/wp-content/uploads/2006/07/Hen%20Houses_008.jpg
I hope this will clarifies it up.
That's what I was thinking you were talking about...as flgardengirl stated, those aren't made for roosting, they're made so...
You'll need to raise them so that they're higher than the boxes. Here's a thread with some pics of inside coops and their roosts. https://www.backyardchickens.com/forum/viewtopic.php?id=316494&p=4
If you don't have room to place a roost higher you can always lower your nest boxes and put a...
Are you using the bottom of the nesting box for your roosts? If I'm hearing you right you are. Those are not meant for a bird to roost on, just to help them step up into their boxes. They'll naturally want to roost in the highest spot in the coop.
Find yourself a 2 x 4 and place it wide side...
Are your roosts higher than the nest boxes? If not you'll have to move them up.
I had one broody hen that wanted to sleep in the nest boxes. Each night when I locked up the coop I'd take her out and put her on the roost. Took a few days but she finally got it.