The fix I made mention of before in my previous post was not an "L" bracket, but a threaded bolt that they put through the flap, and into the square channel bracket which is behind the flap. The flaps have one bolt usually in the lower outer corner. We added the second bolt in the middle of the flap and into the channel. It is the flap hitting this channel that causes the noise. I can send a picture if you need it. I would attach it to this reply, but I do not see a method on how to do it. Hope this helps.
2012 Berkshire 360-FWS
2003 Jeep Liberty Dinghy