How often do you scoop the box? Are the litter boxes covered? Some cats hate the smell of their own poop so much that they would rather go elsewhere. You may need to scoop more often and remove any hoods on boxes.
Also, have you switched food recently? This can make poop really stinky as well. A friend of mine's cat was so stressed with the addition of new cats to her home that her intestinal bacteria went all askew. This caused her poop to stink very much and so she refused to go in the litter box. So you may want to get a vet check to make sure there isn't a medical reason for this.
In addition, make sure to clean the spots with enzyme cleaner to get rid of the smell. Even though kitty isn't going in the same spots right now, you want to prevent that from happening.