There is a very interesting study that suggests many boys are being left behind because they waste their time playing video games rather than studying. Girls play a lot less video games on average. Because at the end of the day, the system may be better suited to girls, but the system hasn't really changed that much. What has changed is that it's more common for girls to go to uni now, and other external stimulus such as video games have popped up.
And finally I just want to add that it's not always the school's fault. If the guys want to be rebels if they don't care about school, that attitude is the parents' fault as much, if not more, than the schools'. And if there is some sort of sexism going the other way (such as more female teachers so on average in schools girls are preferred) then do something. Don't whine about it saying boohoo boys are being left behind. I once had a female teacher like that. I went home and ranted to my parents and you bet they went to that teacher and made her feel small.