We have the same issue with our front window gasket.
I have not been able to remove the stains with any products I have tried.
Something we have to learn to live with in the PNW I guess??
I have tried to leave the rock guard ajar over the winter so air would circulate but for the last two years it has been closed by others!
If I remember correctly I drilled a couple of small air holes along the bottom of the cover, to allow some air, when this happened the first time to me in my 19.
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Jim
Sometime life gets in the way of living.......