I would be searching hard for something that is causing her pain once a rider's weight is added to the equation. Has she had a vet workup? Has a chiro seen her? Does her saddle fit her (not only through the gullet, but through the panels, length, etc.)? Saddle fit can look passable without a rider, but really go downhill once there's weight in it. You didn't say what style you ride, but if you're riding English is it possible that the flocking has lumps that could be digging into her?
I've never owned a mare, so take this for what its worth, but I have heard/read that ovarian cysts or similar issues can cause them a lot of discomfort, especially when the weight of the saddle starts pressing on their backs.
It's very possible that it is a training issue, not a physical one, but ruling out the physical tends to be a good place to start.
A stubborn horse walks behind you, an impatient one in front of you, but a noble companion walks beside you ~ Unknown