I bought a vintage Trek frame and was building it up with a modern Ultegra wheelset when I noticed that the rear wheel was about 4mm off-center of the brake nut. My first thought was that the wheel spacer was on the wrong side of the wheel, so I tried threading the axle through the hub so I could place the spacer on the other side. The result was that the wheel was now off-centered to the other side. Feeling that I had a bad frame, I took it to the most seasoned bike mechanic I know. He took a bunch of measurements of the frame and everything looked good. He told me that the bike should track fine because the wheels are in line, I will just have to adjust the brake pads accordingly.
It sucks because the seller of the frameset surely knew about the misalignment without telling me. Has anyone any ideas about what could have caused this?