In my experience the City setting just takes most of the dead travel out of the top of the throttle pedal's action. So City-3 definitely shouldn't feel as you describe.
Have you tried the adaption process in the PB+'s instructions? I'm thinking that if there is an issue with your PB, running this may reset it to your car.
Alternatively, it may just be that you're used to large initial throttle inputs, as per Watts' advice.