Try diatamaceous (sp?) earth. I would buy the human form at a health food store. It kills the ants without hurting higher animal forms. You sprinkle it all around and in the stall, they take it back to their nest, and it cuts them all up. Been using it here for the ants, but our horses are all outside.
I would call the vet to do a lameness work up, and decide on tests from there.