There is a spot on the rear ones that you have to move the slide nut to so it will sit flat. Slide nut being the thing that moves inside the rail for the rear crossbar to bolt to where you can adjust the span. There is an area in the cover to move it to so the cover will sit flat. Look at the underside of the cover and you'll see where to move the slide nut to. Then it should pop in and sit flat. Also there is a short filler piece for the rail you have to pop out.
Hmm...I removed the slide nut completely. Will put it back in and see if it makes a difference. Will also look for the short filler piece for the rail. Will report back. Thanks for the response!