First - nice looking horse.
It may well be a combination of things going on with her that need to be resolved. I agree with Saddlebag - mouth is not in a good place yet and her feet may be sore also. With regard to the saddle, from what I can see is that it does not seem quite right at the back end in that it just looks like it is not sitting 'flush' (please bear in mind I haven't got my new glasses yet so may be missing the obvious). That means when you're on her, then the saddle is pushed down on her back more and hence may be uncomfortable or touching unevenly. I also feel there is not a great deal of wither clearance. So, further investigation is required. Can you post pictures of the back view?