We were having the same issue. He was supposedly paper trained, but he rarely used papers here. He was going pretty much anywhere and everywhere. I, too, have had to throw out rugs and got the not so nice smells in the house. We tried wee wee pads and sprays and whatever. We finally found success in letting him roam leash-free in our yard. He just wanted privacy. He rarely goes in the house anymore. Good luck to you. I hope you find your dog's potty secret soon.