Hmmm, when we were building my coop, I read on here somewhere that it is better to put the flat side of the 2 by 4 face up, so they will have a broader base to roost on, to maintain balance and keep feet warm. Guess it works both ways.
But I was going to say that when my chickens were young, they huddled in the corner to sleep, and poopy butts did not result from it. The poopy butt thing may be some slight imbalance in their digestive process. You might try organic apple cider vinegar in their water for a while, about a tablespoon per gallon of water. That has cleared up many a poopy butt. Of course, you may have to clean up their behinds once, to get it out of the way. Clipping is very effective.
The flat side of the 2x4 is actually not good for their feet. In fact the Journal of Horticulture and Practical Gardening says that their perch "should not be thicker than they can grasp with ease, as that would occasion them to be duck-footed". If you watch, many chickens who have to roost on the flat side of 2x4s will often perch right on the edge so their feet wrap around the front. Following is some more info...
Tendon-Locking Mechanisms
When birds land on a branch and their legs flex, the tendons begin to lock. Flexor tendons lock automatically when the bird's knees are bent and do not unlock until the knees are unbent. The tendons then lock the toes to secure them around the branch. When birds begin to fall asleep, their instinctual tendon-locking mechanism simultaneously begins to react. As they fall deeper and deeper into sleep and can no longer hold themselves up, the tendons lock even deeper.
The bird can stay locked and in place with no effort at all and no stiffness because of the flexor tendons. They are narrow strips that extend down the leg muscles down the back of the tarsus bone and to the toes.
Why Birds Sleep Perched
Birds sleep perched as a safety method. They tend to sleep at night, perched high on a tree to avoid predators. Web-footed birds like ducks do not perch, as they don't have the tendons to lock onto trees in the same manner.
About their feet getting cold, try this experiment, go out to your coop on a cold evening when they are already gone to roost and slide yur hand up under their fluff feathers and feel their feet. They will be quite warm. Also, pick up your chicken and bend their led at the knee and you will see their foot draw closed. This is that flexor tendon working. When they roost, their knee fully flexes causing that tendon-locking mechanism to engage which keeps them secure on the roost. That is why they don't fall off when they are at rest.