My experience with the deep litter has been the same. It gets slimy and I've even found mold growing in the wetter parts. In the summer the flies were horrible as well. It works better for me to clean every week and compost it all outside the coop. We have a pile about 100 feet from the barn where it will compost all winter.
The entire coop is covered with a roof so no water is getting in that way. The wind still blows the rain in, and wet chickens make the bedding damp after they come in from free ranging. I just think it is better to offer them clean, dry bedding than trying to do deep litter.