The study cited does not prove that the academic system is not biased towards female students. In the study, the academic gap still appeared, it just appeared much later, in the ninth grade.
This would suggest that it is the school system itself that is having an impact on the gender academic gap. Why were boys that were excelling in school until their teenage years then falling behind their female counterparts? Most likely, because the school system left them bored, stifled their competitive streaks and strangled them into conformity. When they wouldn't go along with it, they were punished, missing more school and falling further behind.