Mosfet Driver - High Side Output Problem
I would debug this in two separate pieces, starting with the following ...


As you're doing six-step commutation, you can should verify that you can command a commutation state on your Arduino and you see the right outputs on the six PWM outputs. Be sure you review typical six-step commutation strategies ... where you basically have three states: PWM, ON and OFF (high impedance)
Drive a single pre-driver and bootstrap with a function generator. Do you see the same behavior?