I took the bike to the LBS and the tech worked on the back brake while I watched. He sanded the pads, scuffed the rotor and made some other adjustments. He also cleaned everything with a special degreaser that doesn't leave a residue. He took it out to the parking lot and didn't hear the noise, as I suspected he wouldn't. The noise doesn't show up until the friction starts to increase in the brakes. I took it for a longer test ride (maybe 5 minutes) and as the brakes started to grab more, the sound came back. This is not a high-pitched squeal. It's a loud vibration that you can feel through the bike. When I got back, the tech heard the noise and said he would talk to Trek about warranty service. I left the bike there a few days ago. I'll call the LBS today to see what the plan is.