arduino power problem when using boost converter
From your setup, I assume that the motor (not only the driver) is also being supplied by your booster. At start up the motors draw a lot of current, thus dropping the supply line voltage down to a point where the RESET pin of the arduino is active. You could do one of or a combination of the following:


Add a capacitor at the input of the motor (or increase the already existent), in order to cope with this in-rush current. 
Add a diode / rectifier at the input of the arduino and a capacitor after that in order to prevent the motor from drawing current from the arduino's input capacitance.
Add a current limiter to the motor line, e.g.: a) NTC thermistor (Keep in mind that it becomes useless if the motor is turned on/off/on very within a short period of time) or b) an FET / BJT based current limiter. Both solutions will add to the power loss in the system.