I put sand in my coop after an exceptionally wet spring and the mud was nasty smelly. Once I had sand the only time it smelled was when the chickens scratched down to the mud. Once summer dried everything out I never had the smell again. Don't know how long you have had sand but you may need to change it all out after your run dries out real good. Now I am relocated and the birds can free range daily which really has put an end to smelly run issues since the run is used only on occasion now. So if you can free range them it helps tremendously. Of course if you are limited strictly to a suburban backyard that really isn't much of an option. Good luck with the issue.
I have a chicken tractor... So I just use the sand in the coop.... I put some DE down last night , this morning the smell was normal... I guess it was just from it being wet... I've only had sand down for a month and added and scooped some out.....