Sounds like a possible Crank Position Sensor acting up. They tend to fail when hot and work again after the engine has cooled. Search here for CPS and there are numerous threads / repair diy's.
Here is one of the threads:
http://986forum.com/forums/boxster-general-discussions/66083-help.html
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'01 Boxster S (purchased new) triple black, litronics, cruise, heated seats,18's.
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