I emailed Pedro (
http://www.pedrosgarage.com) and thought I'd share his solution in case anyone else has had this problem.
"The Boxster does not like the accelerator depressed before or during start up.
If the accelerator is depressed, the throttle positioning sensor tells the DME that the throttle is depressed and it automatically goes into safe mode, cutting back on the injectors and retarding the timing. That's why it takes so long to start.
Just depress the clutch (or brake if Tiptronic) and start it up without depressing the accelerator at all."
Out of the dozens of mechanics I contacted, Pedro was the only one who knew I was unintentionally putting the boxster in safe mode, thus requiring more gas at start up and sometimes causing the car never to catch.
No more start up issues!