First things first, have her checked out medical. Specifically for urinary tract infections.
Second, answer a few questions for me. When did this start? Other than you moving in, has anything else changed (brand of food, brand of kitty litter, location of the litter boxes, location of the food & water bowls etc). Has she been spayed? How many litter boxes are in the home? (Rule is 1 litter box per cat, plus 1. So for two cats, you would want 3 boxes)
Along with cleaning with a green machine, you need to use something to actually get rid of the smell. To your nose, the smell may be gone, but to hers, she can still smell it. Use something like Natures Miracle to clean any spots (you can get it at any pet store). I would also recommend cleaning any old spots you can find with it as well. Now, if all of her medicals check out, you can try retraining her to use the litter box. It's time consuming, but it usually works for those that are willing to take the time. First, start off by putting her in a small room with her litter box and food and water. Laundry room or bathroom (no closet obviously). Leave her in there until she begins using the litter box consistently. This can take anywhere from a few days to a couple weeks, depending on the cat. Once she is using the litter box consistently (I like to give them a couple days of not going outside the litterbox) you can start letting her out of the room for short periods while you're home and can watch her. If she goes outside the litter box again, back into the room for another day or two. If she continues to not use the litter box while out, keep her out for longer and longer periods. Eventually, she should be able to be allowed back out into the house full time. I will caution you though, make sure all spots are thoroughly cleaned using Nature's Miracle or a similar product. If spots are cleaned properly, this won't help at all.
