PWM on Arduino mini Pro

Hello

I had bread-boarded a stepper motor using the Arduino uno and the Pololu A4988 stepper driver and the code below was working fine off the digital Pin 3 as pwm.

Now that I'm using the MINI Pro it is not working, it is acting as a regular digital pin. I no longer see pin 3 pulsating from 0 to 5.

I used the code from this Maxuino link:

http://www.maxuino.org/stepperdriver

Do I must make any changes to the code with the mini pro to get PWM to work?

does the stepperdriver.h works the same way or are my missing something else?

Thanks. I just started playing with Arduino last week.