The spatial awareness difference between the sexes is very well established in the literature (another is that women are socially more sophisticated) but I don't believe there is any firm conclusion about why it is so.
I can tell you that a friend of mine did research into this topic in the context of "learned helplessness", which is exactly what it sounds like: people do indeed learn to be helpless at particular things, and it looks like this plays a major part in the lack of spatial awareness skills.
You can provide spatial awareness training for people, and interestingly, whereas men generally see a small benefit from it, women can experience one of two things: a big benefit, or an actual loss of ability. This ties in with the "learned helplessness" hypothesis. One of the issues is that training has to address the fact that the person has this problem, otherwise it will reinforce their received mental ideas. ("I got that thing wrong, it just goes to show I can't do this, I should just give up now ....")
My impression is that if you take steps to deal with the "learned helplessness" phenomenon, you will see differences like this vanish.
It's not so different from the medical study of caffeine. The research was believed to show a positive effect on alertness from caffeine intake. Then some bright spark realised that the people in the experiments hadn't been screened for coffee- or tea-drinking. New experiments were carried out in which all subjects went cold turkey on caffeine for several weeks prior to the experiment, and no caffeine benefits were observed. The "benefit" in the previous experiment was simply not suffering the side-effects of existing addiction.
Studies which don't compensate for phenomena like learned helplessness are probably going to run into a similar problem.