From my experience - You have to make sure the axle is properly seated in the dropouts. Loosen the quickrelease and make sure the axle is seated properly before tightening. This is best accomplished with the bike upright and the QR loose. Sometimes the "lawyer lips" are an issue. I never have a problem with the pads incorrectly hitting the rim. That relationship should not change unless the wheel is not seated in the dropout correctly or the pad itself is loose. What I often find (my hybrid has some OEM Tektro V's) is I do have to readjust the centering screws to recenter them after removing/replacing the "noodle" in the bracket, but I also like my brakes adjusted with very little lever travel so the pads are quite close to the rim. This makes the centering more critical. Sometimes if it isn't centering quite right I just work the brakes a few times and it corrects itself, or at least closer.