Some repop sheet metal is thinner then what these cars came with. That could be the issue. Are your quarters sprayed with undercoating in the trunk? The factory sprayed a thick layer of undercoating on the trunk side of the quarters in order to limit the flexing you are talking about. If you don't have any undercoating in the quarter, I would spray some.
The same goes for on the back side of the fenders. The undercoating is there to protect the metal from flying rocks.
