How old is she? The reason I ask is that I remember when my son was about 12 or so and he would wake up in the middle of the night, crying in pain. It was in his legs and trunk area from what I remember...and the doctor could not find anything wrong with him. Chalked it up to growing pains.
It went away as quickly as it came, but freaked us out all the same. I hope this is the same for your girl!