Compensate by adjusting the PWM value of a particular motor? That's a good idea!
What kind of battery would you recommend to power the motor shield? At the moment, whilst I'm getting my bearings I'm just playing around with 6 regular Alkaline AA batteries but what I've heard is that these may provide an unreliable current/ current drops off quite quickly. I looked at LiPo but they seemed quite expensive at JayCar (~$70 for 12V 3600mAh). Is a regular 9V battery ok for supplying power to the Arduino board?
Thanks for you're help!