Emily used to have a "little problem" like this and I used the Nature's Miracle. It turns out that stuff didn't quite get rid of the odor for her (after all she is soooooooo sensitive ), so she would go back to the same spots. I switched over to Woollite Pet Stain remover and that seems to have done the trick.

Regarding the behavior problem, I have no words of advice. I am planning on replacing my flooring in the next year, so I am definitely interested in how you take care of things...