Well according to that pic, there's a whole lot missing....
You need to provide 5v and ground to the MM to give it power, and you need to provide control signals to that section called Control Zone in the middle.
What exactly are you pwm-ing?.... have you shown all connections?
And your code too, would probably help
Edit... if you look at the manual, you need to provide a high/low or low/high pair it In1/In2, as well as high to EnA... the EnA high can be pwm'd, it's what gives the motor it's speed control....
Sorry that's mostly crap... I don't use mine as a shield, I have it loose... yours is obviously plugged on top...