I'm not sure of what type of adjustments can be made to your brakes, but IIRC about brakes in general, the pad should not contact the rotor all at once, or perfectly flat, if you can visualize what I mean.
I think on "tip" of the pad, likely the top?, should touch first by a hair, it's kind of like the pads have some toe-in.
Having the pads at a SLIGHT angle to the rotor on first contact make a huge difference, for example, on a bicycle wheel.
I could be way off, I've never had to do anything more than swap pads myself, and mine had no problems.
Just a shot in the dark.
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