Some mares are extremely sensitive with their back ends and need very little to set them off. Just watch when she comes in heat, as she may have cysts which are painful and can be most of your problem. Her heat cycle should be @ regular intervals without any, stress,anxiety, behavior changes, discharge cloudy-yellow in color. If it is not as easy as that, you may have either medical or hormonal imbalances.
You say she is good with her front feet, what about grooming? Start there, Stand facing her rear, keep your left hand[if on horses left] on her side[flank,hip,croup...] brush down the leg. Make sure you stay slighly in front of her leg and keep your hand on her, you can feel her tense before she lifts leg to kick. If that is ok, use your hand instead of the brush, go down the back of the leg gradually increasing pressure until she picks foot off ground. As soon as she does, release leg and do something else. Go slowly 20-30 times per grooming session, and do both sides equally. Each time hold it slightly longer, but don't try to force it up and hold on tight, that will make her resent it more. If you think it could be a pain issue, try giving 2 grams of bute prior to grooming, if you have no kicking, you might be dealing with pain.