It's probably a combination of factors that make "the female founder" seem more rare than she actually is.

There is a breed of female founder that lives to pose for cameras and magazine covers and to be mentioned in Valleywag. But more common are those who are happy to grow their companies to a certain point that is manageable enough. They don't want or get a lot of attention, which makes them seem more rare than they actually are.

Maybe the core issue is that females don't tend to form the kind of companies that tend to get really big really fast. Each iteration of a growing company changes the social / cultural dynamic of a company, too; these are areas which females tend to treat with more care.