I would start by the tail lights and see if the relays that confirm that the lamps are on are working and there contacts are good. Then check the wiring between the contacts and ground and then the wiring from the contacts to the front of the car. The Electricial Trouble Shooting Manual is very helpfull but the Service Manual would be enough to to get it figured out.
I also had this problem recently. Every once in a while the 3rd brake light on the dash will come on but all lights function.
It comes on occasionally but I don't pay attention to it. More of a distraction than anything else.
I think I gave the guys at Autowave a headache because my car had the same issue. After checking all over the place turns out the sensor was bad and no longer available. So until I find a new one, I just had them disconnect it. :tongue::biggrin: