Thank you for sharing those photos. Get her out of that saddle ASAP! It is way to wide in front and if you cannot get even a baby finger under the pommel unmounted, imagine how much pressure is on the top of her wither bone with your weight in the saddle! Now , mulitply that with each trot step, and if you are not a balanced rider, then the mulitiplication factor goes up even more. That saddle is probably the root of most of the bad behavior.
On the good side, this means that when the problem is taken care of the mystery is solved. On the bad side, it may take awhile for the soreness to go away and she may be saddle sour for some time even after you geet a better fitting saddle.
Just out of curiosity, how did your horse and that saddle come together?