If it is happening with both handles, I think you should take a look at the cable of the window regulator. They are known to stretch and can be finicky. Pelican Parts has a great tech article on this. I have replaced both of mine. Reasonably straight forward project. No special tools, just patience and getting your head around all that is going on with the switches and the cable, door open/closed. Keep posting what you find on your quest.
Porsche Boxster Window Regulator Replacement / Window Switch Replacement / Window Motor Replacement - 986 / 987 (1997-08) - Pelican Parts Technical Article