Ok I will take the serial commands out of the interrupts, set my variables to volitile, and question my use of interrupts all together. About the decoupling cap in my power supply, I am using two 12v sealed led acid batteries powering the motors and driver alone would I need a cap, could there really be that much noise in that circuit? What about the hall effect sensor? Could the magnets in the motor be causing such a large jump in the click count? or is there something else happening?