What are you using to clean the cage? I find vinegar works well to neutralize any urine odours. My buns live in my living room, and they don't smell at all. I clean out the cage and litter boxes with a 50/50 vinegar water mix. Just use a spray bottle, mist then wipe up.
There is also the possiblity of a hidden urine pile somewhere. Have you checked under the cage and all around the cage for urine? Sometimes buns can spray (even females) urine or pee over the edge of the plastic bottoms. The only time my guys smell bad is when someone pees outside the litter box.
--Dawn
