What Causes Pain On The Base Of Skull?

I have pain at the base of my skull when I lay on my back making sleep torture sometimes. I've had an MRI and my doc says he doesn't see anything that someone my age would normally have. I have military neck and I've had whip-lash late last year - after which the sleeplessness was increased. Many days, I'm like a zombie. I'm going to a physical therapist which is helping some muscular problems associated with my contortions in bed trying to get some sleep, but I still have the pain in the base of my skull.