KBB rarely reflects the market price for Porsches accurately. That said there are a lot of Boxsters out there and the difference in price between an early 986 and a late ('03-'04) isn't that much considering what more you're getting (especially comparing an early 2.5l to an S 3.2l). As I'm sure you've seen I'm working on selling my '99 and the market is slow. I've had a couple local lookers, but most of them then realize they really need more than 2-seats.
You're '99 is very low mileage and usually that is a good thing, but Boxsters are drivers' cars not collectors' cars. Unless you've retrofitted the IMS bearing and other known problem parts, a more informed buyer might be leery. That said any 986 Boxster is a hell-of-a-lot of car for $10-12k!
FWIW, I bought my 993 at approximately double the KBB value. In fact I had to get it appraised for lender/insurance reasons, so that a real market price was known for the vehicle. The appraisal came in above my purchasing price, so well more than double KBB.