im no expet and it is hard to tell without pics, but is it possible that the "She" is actually a "He" and one of the hemipenes for some reason is unable to retract? ive heard of this happening before but im not sure if this applies in your case or not. only other course of action i could recommend would be to have the snake anestethized (sp?)and then examine him or do an xray or whatever it is they do to reveal muscle tissue.
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