How does she respond when you brush/groom her? Does she flinch and nip at you when you run your hand/brushes along her back??
Pain aside, I ride at a barn with lots and lots of lesson horses. They come up with all sorts of things to do when they have a child on their back. Rein rooting (which nearly rips children right out of the tack), crow hopping, ear pinning, you name it!
Sometimes a horse can be downright moody. Help from a qualified trainer might be worth your dollar and time.