The sound may have been unfamiliar to you because you perhaps have not sat in that area of the cabin before(?). I recall a while back, sitting in First Class on a 747 for the very first time and heard a noise which sounded like a bandsaw just after takeoff. I realised, shortly after my initial shock, what it was (the tire rubbing against the brake pad), but it did take me by surprise.
I'd say that smaller aircraft tend to put you closer to the "action", so to speak.... So, generally, the noises will appear louder.
Not that I'm saying there _wasn't_ anything wrong with the flaps...
Rgds.
Q.