I had a 2000 Boxster and had this problem. Mine came in the crease of the first fold. It really upset me at first because I thought the top was ruined. I now have a 2002 Boxster S and have the same problem. I went to autotrader and closely examined pictures of Boxsters with the top up. I found many of them had the same problems I had. I don't know what is causing it or what to do to improve the condition.
Tom
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