From what you described, she's low withered and wide backed, do you know if the saddle you're using is a medium or wide tree?
Sounds like, with the rocking (I could be wrong), that the tree is too narrow and is pinching her. If you add padding that's only going to compound the problem, like putting thicker socks with already narrow shoes.
Is there anyone that has experience with saddle fitting that can look at the saddle on her and give you some advice. Sadly an improperly fitting saddle can cause many issues with a horse .