Windows and interior trim can be prone to squeaks and rattles. Numerous, small adjustments may resolve the issue. Additional creaks have been attributed to front and/or rear window fit as well.Google+
Car Problem Reports
Porsche Boxster S Windows/Interior Trim are Prone to Squeaks/Rattles
Porsche Boxster S Problem
Visitor, 2009 Porsche Boxster S, 29,000 mi
I used a dry graphite lubricant and sprayed the inside of the drivers door and the rubber gasket at the top of the door. Seemed to work great. I also suggest using a painters tape to prevent over spray.