*Assuming* you've trained & are asking/riding her well, I would think it is probably something physical. What exactly did you do to 'rule out' medical problems? Perhaps something was overlooked or discounted prematurely.
But if it's purely behavioural(& in humans we tend to think of 'stubborn' as persistant and a good trait
), especially when you speak of 'not being able' to use a crop, certain spurs, etc, I think it's likely it's something you may be doing/not doing, or there are 'holes' in her training, so getting a good trainer/instructor to come help you both would be helpful.