I didn't run into this problem at all. Did you maybe miss the plastic spacers or maybe the metal shims or something on the 4 "GOBI" logo brackets?
it's supposed to be from bottom to top stacked directly on top of the metal in the roof gutter: 1 skinny rubber pad, the two white plastic spacers, one wide rubber pad, one metal shim that has rubber pads on it, another skinny rubber pad, and then the "GOBI" logo bracket. on top of the bracket and between the rack is another large rubber pad. Then the rack. On top of the rack goes the washer and lock washer.
Also, make sure the front brackets are on the correct side. There's a driver and passenger side for the front brackets. If that is reversed, the rack will not sit flat like you said. If all of that is there, maybe the rack is warped or bent?