warped rotor?

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true warped rotors are rare; usually runout difference is the result of pad material build-up and hot spots. if your rotors are fairly new, this shouldn't be a problem. i'd be looking at wheel bearings and tie rods.

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to answer the caliper rebuild stuff: when the inner seals go bad, they get soft. the inner seals actually retrac the pistons when you release the pedal. if they get soft, the pads don't retract and ride on the disks. this causes heat build-up and fade. i doubt if this is your problem. at any rate, if you want to rebuild the calipers, the dealers will NOT sell you the inner seals, only the outer dust boots. the best place to get seals AND dust boots is here:

http://www.zeckhausen.com/Brembo/Consumables.htm#Rebuild