Is there a hen or two in your flock that doesn't have the featherless bottom? If so, they are likely plucking the feathers out of the others. If chickens are too crowded (in coop etc) they feather pluck, bully, and in extreme cases resort to cannibalism. If chickens see "red" as in plucked areas or wounds, they will continue pecking at it. If you could get some Blu Kote as the feed store. cover the bald areas with it so it doesn't show up red.
Given that you've eliminated lice as the problem, X2 on both of the above posts. You may need to reduce the number of birds in your coop and definitely coat their bottoms with Blue Kote Wound Dressing. Not only will it prevent infection and promote healing, but the bad taste will discourage the other birds from pecking at the area. In addition to hanging treats, you can also hang shiny things like CDs for them to peck at and put log structures into the run for them to climb on as a way to alleviate boredom.