I apologize. I misread your post initially. I don't have deep litter in the run. It was lawn until the girls ate it all.... And then just hard packed dirt.@Murdy How long did you let the run deep litter start to decompose/breakdown before you choose to till the ground?
Although I didn't have a smell, I noticed that it took a week or two for everything to start breaking down and a composting effect to start to eliminate a fly problem I was having in the beginning.
I add a bale of pine shavings/leaves/grass clippings every 2 to 3 weeks just to keep things fresh, so that might be the trick too.