You might be suffering from uneven pad deposit (search this). It is tough to warp the stock M3 rotors, but easy to overwhelm the street pads. During press release days for the E9X M3, BMW installed ceramic pads in the stock car.
This happens to all novices transitioning to intermediate and indicates time to switch pads and brake fluid to higher spec racing fluid for track days. Braided steel lines help too.
[Gearhead beat me too this]