Several things could be occurring for your mare. Some possible reasons why she is reacting as she is:
1) When mares have ovarian cysts, they can become extremely sensitive to wearing a saddle and bearing weight. Generally, this would extend to the riding experience, whereby she would be irritable and possibly react in odd ways due to the gaits and activity you were asking her to preform. If this is suspected, then you should contact your veterinarian immediately to evaluate her health.
2) However, if all you are getting is a little disenchantment from her when you saddle, then it is probably not ovarian cysts at all, but rather her way of letting you know that something is not comfortable or that she would prefer to be left alone. Although you checked and cleaned the pad, you might evaluate whether the pad is thick enough to provide adequate cushion for her back. Assuming you are riding Western, a thick working pad with your doubled wool pad on top is a preferred use of saddle pads. Or you might invest in a thicker pad that can be used alone. Additionally, the saddle you are using may be pinching her withers and causing discomfort if the saddle is too small or is just a bad fit.
It is good that you are concerned about this behavior and are trying to figure out how to eliminate the horse's discomfort. However, even if everything is perfect, your mare may just be exerting herself during the saddling process. If this problem persists, you should consult a professional horse trainer who can observe the saddling process and provide you with some assistance.
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