Doctor says I don't have stress fracture, but my shins pain won't go away?

About half a year ago, I had a precursor to a stress fracture, but I rested for a while and it healed. I started running again, and began too quickly so I started getting the same shin pain again. I stopped running and got a nuclear bone scan, but the doctor says that my bones have actually healed better since my last injury. So if I don't have a stress fracture, how do I still get such pains in my shins when I start running or even when I climb up stairs? Did the bone just heal badly, because the doctor saw no abnormalities there. What can it be?!!