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.
Car Problem Reports
Porsche Boxster Windows/Interior Trim are Prone to Squeaks/Rattles
Porsche Boxster Problem
Average Mileage: 30,050 mi (15,000 mi - 45,100 mi)
Visitor, 2003 Porsche Boxster, 15,000 mi
Constant mild noise from the top of the drivers door panel. Sounds like a loose cable.