I know that if you've been giving fruits and veggies to bunnies, because of the way they break down the beta carotene in them it causes a urinary discoloration, (red urine). I've found it to be slightly more unpleasant. Perhaps someting similar is happening?
I have noticed that my female Lacey has much stronger smelling pee than my male Starsky but she has always been like this. Has your bunny always had smelly pee or has it happened recently?