After quite a bit of waiting for the bike shop to do enough testing of the brakes, Trek replaced my bike frame under warranty. I understand that they wanted to make sure other options had been explored before going to that extent, but I was very glad when they finally decided to do it. I knew it would fix the problem because no amount of brake adjustment had made any difference. Several of their mechanics had worked on the pads and the rotor, and the noise kept coming back. After they would work on the brake, I wouldn’t hear any noise, mainly because there isn’t any friction between the pad and rotor at that stage. As I went through the bed-in process, the brakes would start grabbing more, and I would start hearing a slight harmonic sound. The more I tested, the more I would hear the harmonic tone – not loud but it was there. Eventually, I would get a loud harmonic honk when I applied the brake, as loud as ever, vibrating the whole frame.
Here is a picture of my previous frame. Note the position of the back brake, and where it bolts on.
This is the new frame, a 2013 frame. The brake is attached in a totally different place.
The braking is excellent, with no noise. I love the bike now and highly recommend it. Thanks Trek and thanks to Cycling Spoken Here in Cary, NC for helping me work through this problem.