It could be a number of things but I agree with Sash , balance will only help .
To balance , you could try deep cleansing breathing of energy from crown down to try to purge energy out of the rear of the heart and from your feet .
If it is energy built up in the male tan tien ,this can be eased by using up the energy to meditate , heal or to project for example .Just draw it up to your heart to send it down thru your palms to heal . You can also lie down and use the excess energy to vibrate out and OBE .
If it is kundalini ,then sitting in regular meditation until this event passes should allow it to come up naturally and smoothly . Qi Chong does bring up energy especially if you are breathing yoga bandha locks in conjunction with Qi Chong . Suppose you ask your Yoga and Qi Chong teachers for advice esp re blockages and breathing to balance and purge .
Psychically when the root chakra throbs it can mean" home in danger" . Although , this may not be so in your case . I had similar symptoms and could feel waves of energy emanating from the red chakra also on the arvo before Sept 11 2001 . My spiritual mentor explained that the red chakra throbs like that when homeland is in danger in some psychics . She said she had had visions that something bad was going to happen in NYC and that I felt it too because that was the land of my birth ( We were both in Australia then .) Since then when it is painful as you described , I look to the relatives at "home" and see what is going on there. The root chakra played up when New Orleans died too . And I prayed and white lighted the area in loving intentions. It can't hurt .
You could also consult a doctor again if it continues to play up and make sure there is nothing wrong healthwise .
Finally a blockage of energy could cause this too . To clear blockages , you can try yoga , drink lots of water and learn pranic breathing .You can learn to deep clean and purge . You can use NEW in that area concentrating on releasing energy instead of bringing it in and building it up .
Here is a link :
http://groups.msn.com/AlchemicalFlame/s ... hotoID=137
~*~Love , Light & Laughter ~*~
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