I have the same issue with my 2010 VLX. My dealer actually caught this when I took it in for service. It is the factory cover and only happens when left in the sun. I keep my boat under an awning, so there was never any issue when I would pull the boat out and go. At the dealer, the boat was left outside, and when they pulled the cover off, the vinyl was stained black. When left in the sun for a few hours, it goes away. I also left the cover on at the river one day when we didn't use the boat, the next day the same issue. He said it is a defect with the vinyl, and they will warranty it out and replace everything. He said just bring it in at the end of the season and they'll take care of it. check with your dealer
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