Ok, here's another idea, I have heard (and through personal experience) that the metallic brake pads emit dust that can land on the back hatch and with a little salt can start corroding. I can remove the it with a little wax because it is not really the hatch that is rusting but a piece of metal on the paint. It just leaves a stain, if you will, that can be waxed (clay magic works too) away. I think the same is taking place on the step rails.
So if I can't find something to remove the stains, I guess it is back to the dealer to try and work something out. Thanks.

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2001 XE Silver Ice