^ what do you mean by change the wires? did you interchange the little black boxes? If the problem still persists after swapping the boxes, then there are 2 possibilities.
1) the actual tail lights are faulty. Take them out and swap it with the working ones. You can just hook them up to the opposite harnesses, no need to mount them on the car(which would be impossible without breaking them). This will decide whether you need to go to step 2.
2) trace and check the wiring coming to the black boxes from the third brake light, or the other working tail light. I am not sure unto where you will need to trace for the wiring, I'm sure some one can give you a wiring diagram here.
Do 1) first, so you know whether its the actual lights or the wiring.
PS: The soldering is flimsy in the EE tails, so if the actual tail light is the issue, cut it open and check the soldering, resolver the wire joint points.