I found an interesting read on migraines and headaches over at http://www.migraineprevention.com/
It discusses that
“While the current medical models for migraine pathophysiology include afferent input from the meningeal arteries to the trigeminal sensory nucleus, the effect of any other acute or chronic noxious afferent input from the other divisions of the trigeminal, primarily the mandibular (third) division and how that noxious afferent input effects sensory modulation, has been essentially ignored.”
Then “as a result of genetic properties of the host as a result of a pre-sensitization of the sensory nucleus inflammation of the arteries, which is thought to be primarily responsible for the patient’s pain, throbbing and aversion to movement [occur].”
The site goes into greater detail and also discusses an elevated sympathetic tone in patients.