I don't know if this is 'advice' but I had almost an identical problem. We got Bandit a little young (11 weeks) and crate trained. He was always having accidents in his crate no matter how small it was and how often we took him out. He was always having accidents in the house. When we first got him he was really sick so the first few weeks I don't want to really count. Then, when we walked him he'd go out during walks, but he'd still go in his crate. The only place he wouldn't go was in our bed lol

. After he was 1 he started getting better and then when he was 1 1/2 we moved from the apt into our house and it seemed almost like the miracle fix.
My theories are that he had a lot of accidents we didn't see and therefore didn't put the natures miracle on, or there was a dog in the apt before us that had peed on the floor and the smell was still there.
Maybe you could have your carpets shampooed with cleaner plus nature's miracle? If he's smelling anything he could be smelling it in his crate too? That's just my totally random theory lol. Good luck!