The curve of the roof does not match the curve of the side rails. The middle two feet on the side rails will sit closer to the roof than the outer feet on each corner. Try and get the middle two feet as close to the roof as possible without contact, this will minimize the distance of the outer feet and the roofline.
I've thought about getting bar stock and trimming to fit exactly so as to not use the supplied spacers and washers to shim that last bit.
FYI, If the cross bars are loose, they should not affect the fitment of the side rails. Let us know how it goes.