Doesn't honestly sound like any result of the "root chakra" lighting up. It's always there doing something because it's the lower part of your "spiritual" energy system which we all have and a lot of people would be in a lot of trouble were it the case. People don't get migraines because of the chakras unless some other factor is at play - say, concentrating too hard for too long a time.

Could be that you made some kind of psychosomatic connection between it and your physical body therefore. Could even be something like the perfume someone is wearing.

Badcopyinc has some very good advice.

♥