You may have developed hard spots on the pad surfaces. This is usually caused by excessive heat before the pads have properly seated on the rotors. If the rotors look OK and you may have to check them for runout. (new doesn't always mean fixed), then remove the pads, examine the contact surface and if they look glazed, you may have to sand all of the glaze off to get them to seat properly. This can also cause squealing as well.

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Jeff Lawrence
1989 300e
2000 Dodge Grand Caravan SE
No matter what you fix, there will always be something else to fix..
"Warranty" is just another way of postponing the inevitable.