Shin pain from track?

Ok. So I know what you're thinking... she must have shin splints. But I really don't think this is shin splints. So this started randomly over spring break. I was running through my neighborhood, just a slow jog, when all of a sudden my shin started KILLING. But I kept running thinking that I could push through because it must be shin splints. It hurt really bad when I got back but my knees hurt worse... I have knee problems that my doctor diagnosed as bilateral chondromalacia. Those kill all the time. But anyway, I went to the trainer after spring break was over to have him take care of my knees. I brought up my shin and he said that since it only hurt in one spot that he thinks that it was the muscle rubbing against the bone causing pain. But it hurts even when I'm just sitting down so I don't know. It isn't even really my shin... it's like if you put your foot on its side and move your fingers upward from the ankle bone, it's about 3 inches up on the bone. It comes in terrible waves of pain. Not only do I have to deal with the shin pain, but also my knees. Can someone pleaseeee tell me what's wrong with my shin?