You could be flexing calipers, drums, brake shoes or any number of things. That hydra-boost is probably boosting your brake line pressure far above any real world needs when you are pressing "super hard" on it. I'm not sure you really have a problem as you would most likely never put that kind of pressure on the brakes even in an emergency stop. You would most likely lock up the brakes first but you could test that in a safe area with no traffic/people and lots of run off area.
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