Mine had a very similar problem. When I bought my Supra, I got it “for a song”, so to speak, because it had multiple wiring problems, the result of those wiring problems being that nobody seemed to want to buy it. Fortunately, I’m enough of a geek that I actually ENJOY fixing wiring problems. When I bought the car, the main brake lights didn’t work AT ALL. The third brake light worked, but when you hit the brakes during the day, nothing happened with the main brake lights. If you hit the brakes at night (i.e. with the headlights/taillights on), not only did the main brake lights not work, but as I recall, the left taillight went out completely. Like you, I checked the fuses, checked the bulbs, checked the taillight connectors, and replaced the taillight failure sensor box. None of it helped. Because I was trying to get the car licensed before my temp tags expired (and my friend with an inspector’s license who’s willing to inspect a friend’s car without looking at it too closely…if you get my drift…wasn’t willing to give a passing inspection to a car that basically didn’t have brake lights (I don’t blame him)), I gave up and ran a wire straight off the brake light switch under the dash and connected it to the taillight/brake light wiring harness behind the taillight panel for the sake of expediency. (Those of you on the forum who wish to flame me for doing this, feel free I guess, but it worked…) This was enough to get a passing inspection, but it’s also when the rear lights developed a new problem. The third brake light worked perfectly, but the right side lit up abnormally bright when the brakes were applied, while the left side lit up very dimly. Obviously there was still a problem, and I continued working with it. I got the problem fixed, so hopefully I can help you fix yours based on my own experience.
First, look at the TSRM on the cygnusX1 site for the wiring diagram covering the taillights/brake lights; this will help you get an idea as to what you’re dealing with regarding the function of each wire in the main harness. As Txsupra said, this sort of thing is usually a grounding problem, so before proceeding further, reground your taillight/brake light wiring. Make sure you clean the contacts in the main wiring harness as the next step. Now, using a good multimeter, check both the taillight and brake light contacts in the main harness with and without brake lights being applied. Since you (should have) just regrounded your taillight/brake light wiring, you should have a good grounding point for testing, but I still think it bears mentioning that you need a good, reliable grounding point for all testing. Next, clean the contacts for the bulb sockets as well as the contacts for the plug receptacle that the main harness plugs into. After cleaning the contacts, switch the multimeter to the resistance setting and check the resistance between the contacts in the main receptacle and the contacts in the bulb sockets. The resistance should be consistent across the board. Then plug the taillight/brake light panel into the main harness and again check the voltage at both the main plug receptacles as well as at the bulb sockets just as you did the first time. Again, make sure you use a good, reliable grounding point for testing. Any voltage or resistance variance you find in any of this testing should tell you where the problem is. Rewire the taillight/brake light panels as necessary. If it’s necessary, you can replace the bulb sockets, too.
Hope this helps…
Joe