The noise is infact disrupted airflow so your guesses are correct. Rather than being over the wing it is between the root of the wing and the fuselage. As flap 18 (1st stage) is lowered the air is forced between the gap between the flap inside edge and the fuselage which creates what you are hearing. It seems to be most prevelent between flap angles of 10deg to 18deg when travelling in either direction. This would explain also why a certain amount of noise remains after the initial extension. The running of the flaps themselves is actually very quiet (from experience of extending them whilst on the ground).
But then have any of you heard it whilst you're on the ground and it's happening above you - sounds like the old girl is just about to fall out of the sky!