Initially, I didn't connect the motor terminals, the inverter outputs were floating and the motor was at standstill. The DC power supply that provides power to the whole system was configured to have current limit at three times of the actual motor operating current.
Then for test purpose, I applied six-step gate driver signals based on standstill hall sensor reading (HIGH side PWM and LOW side full-on). Since the motor was not connected, the drive signal could only be one out of the six combinations. However, the DC power supply generated over-current protection.
After I connected the motor terminals and drove the motor in six-step operation, everything was fine and no over-current protection was generated.
My question is, why was there over-current (short-circuit?) when the motor terminals were not connected?
[update] The PWM duty cycle used in both cases was the same.
The negative side of the inverter was connected to shunt resistors shown below and then connected to ground. Sorry for any confusion.