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I did a search and found the top adjustment but anyone have a suggestion on how to remove the black marks. I have used light rubbing compound with no success.
I noticed in the past few months two little wear spots appearing on my tonneau in the same spot as yours. Mine are pea-sized spots where the paint has been worn through, worse on the driver side than the passenger side. I tried the adjustments and doofus-factored it to breaking a part. Replacement part is on its way. Mine will ultimately require repainting.
Can't tell much from your pic. If the marks are on the surface of the paint, you can try some good polish, perhaps with a random orbital polisher, to see if you can remove the marks. If these are through the paint and to the primer or all the way through to the base material, then it's repaint time.