I too have an 07 Base Model that had front and rear "clunks" when I went over slight speed bumps. I tightened all 4 rubber pads on both the front and back hatches and I have been "clunk free" since. Give them a check. When I say tightened I mean make more pressure on the hatch (actually loosen it).

John Phx Az 07 Atlas Grey 5 Speed.