Join Date: Feb 2009
Location: Austin, TX
Bikes: Giant XTC Team Custom XC bike, Nashbar tourer custom commuter
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At least with mounting my BB7s, there was a lot to be said for the alignment of the mount of the caliper. I don't know how common it is, but they have a set of curved washers that let it tilt somewhat on the mounts. The process described in their instructions works pretty well, adjust the brake so the pads are fairly centered, then clamp them down on the rotor while the wheel is mounted properly. Then tighten the two sets of curved-washer mounting bolts and back the pads off the rotor. That way no matter how the mount may be in terms of alignment, it will be properly centered on the rotor and won't rub or brake unevenly.
The critical step for me in this process was being certain that the pads were centered when you do the initial clamp down, if they aren't then it gets aligned to a bad angle, and your brakes will always rub or will brake unevenly on each side.
This could explain why new pads would rub, but to be sure, take a look at the old ones to see if there is uneven wear or a slight angle to the pad face.