Can you add more boards to your coop floor to make it solid, then add some type of bedding? Could be they are getting feet/legs hung up between the slats and that is causing some scrapes or cuts which allows bacteria to enter the foot.
I'm thinking the same thing. A floor doesn't have to be complicated, put some plywood over the existing pallet boards and that'll do. Top with some bedding over that for a softer landing from the roost.
