I've never experienced knee pain while riding duck. For me, duck has always felt the most natural. When I would jump around, or needed a stable stance, while sliding,etc, I'd naturally use a duck stance.I changed my stance several times,experimenting,and never got that naturally stable feeling that duck offered me.
The thing is, I've always been able to do the butterfly stretch cold, touching my nose to the floor. So my hips have always had decent flexibility. Perhaps, you have really inflexible muscles, that are not used to being put under that kind of stress?
Buttering can be quite demanding on that area for sure. It's very taxing, so do it gradually to let your body adjust. I've had those muscles cramp up after heavy buttering.