The musical noises from cnc are annoying..... but are normal and expected.
As for steppers going rock solid .... that's normal as well. The driver is then meant to produce the right amount of currents in the stepper coils to move the stepper shaft around. If the stepper is rock-solid, then it's likely that whatever is upstream isn't working properly (assuming that the stepper is ok).
So..... are you trying to say that the cnc system works fine with the new arduino....... and the issue occurs only when you swap the new arduino with the old one again...... right?