the sound comes from the controller
From the arduino? That should not make a sound.
According to the spec:
The logical part of the operating current range: 0 ~ 36mA
No how much current does your motor take? That is the important value in determing if you can run it from the USB or if you need and external supply.
By re-flash, I mean I need to put the sketch back onto the Arduino.
No nothing should take the sketch out of the arduino once you have put it in. It keeps the same sketch until you put in another one.
I think the HW part is right as I have got it to move
Well it moved once, but maybe you fried it by doing something wrong.
I repeat how have you got this wired up, it sounds like you are not supplying any motor power.