Hello and welcome to the forum. Happy to have you here!
There could be many reasons at play here, that are causing the results you are getting. Firstly, how are you positive that the saddle correctly fits? Does it fit well without any pads on? If so, adding the gel pad is just making it worse...besides, gel pads are garbage. Reason being is because they do not take the force of the saddle, nor do they evenly dispurse the pressure points that the saddle creates. Instead, the gel moves away from the pressure, allowing the pressure points to remain. Gel pads and foam pads, garbage. http://www.horseforum.com/horse-tack...lly-fit-58116/
Also, this could be a pain issue - I would have a chiro come and assess your mares back, poll, jaw, nect, withers, shoulders, hips. There could be a vertibra out, her pelvis could be tilted, who knows. There could be something going on joint wise - have you had xrays done and a correct and thorough vet check to ensure that there is nothing going on in the hocks, stifles, knee's, ankles, back, hips, pelvis - etc, etc???
Another issue that could be at play here, is that she could have a cold back. Do you thoroughly lunge her before you get on?
I would re-assess your saddle. I would hire a professional saddle maker/fitter to come out and check this out to be sure. I would also get a vet involved, and an equine chiro. Eliminate, eliminate, eliminate any question at hand. This could be far more than just a "abuse" issue.
If this horse is friendly with you on the ground, and not so when you get on - PAIN ISSUE screams out at me.