I have had horrible luck with organic material. I have my chickens in a location with little to no direct sunlight (near trees that cast lots of shadows despite having no leaves) and between the rain, depth of material and lack of baking sun it has been a rotting sodden mess. The remainder of the chick crumbles that they scatter everywhere has also been soaked and rotted and I believe is the primary culprit of the stench. It's obviously bothersome to the chickens since they don't scratch around in it... a small blessing, as the number of red worms I found and the leaves I raked out will be more than sufficient to start my compost pile!
I just finished raking everything out so it can dry, and I will be tilling coarse sand and possibly pea gravel into the top ~6" of soil. I am on fine silt/clay land, so it is a big problem. Hopefully the size distribution of sand and pea gravel grains will effectively break up the packing and allow more drainage in the area. I will put a sand layer on top of it all and likely will mix a 5lb bag of DE into the top layer.
I found several great ideas for wet mess, such as digging a cistern at the low point in the run or just outside it. Mine is on a gentle slope from one corner to the opposite, so after tilling the sand into the existing dirt, I will dig out a "creek bed" that runs through the low points and dumps out in a post-hole dug (6-8" diameter) 24" deep cistern filled with broken brick and gravel road debris that I have on hand. This will *hopefully* serve as a drainage channel for rainwater so it doesn't sit indefinitely in the run and soak the bedding.