Another Cover Question

I have a  (black) Westland Sharkskin cover for my boat. Problem with it is, where is rests on upholstery, or some of the upholstery anyway, the upholstery is stained with an purplish-brown stain after days covered in out someone intense sun here in NC. After several hours in the sun, the stain fades away/is bleached out, and you would never know it was stained.  I would still like to keep it from happening.  I bought some white towels and laid them over the back of the helm seat and port combing pad, the two places where it seems to happen.  (does not happen to motor box or starboard combing pad??)  Evens with the towels in place, the staining occurred.  I took the back seat back out a long time ago, because they used to get it the worst.   Last year, per someone's recommendation, I laid a moving blanket over the back of the back seat, which did no good, and strangely enough, one time I took the back seat back off and laid it on the floor, not in contact with the cover and it till happened. Is it possible its not the cover at all and just vinyl that is sensitive to the heat?

Sorry, Thread drift but Cover related sort of. Thought I had a cover leak from the point where the windshield frame meets the deck, had water just in the floor of the drivers seat and area adjacent to that under the area ahead of the passengers seat. Upon closer inspection it seems the water must be coming in through the area around the lifting ring.
Anyone else ever had this? The boat is an 09 Nautique 196 closed bow, no walk through windshield. Thanks for any thoughts.