> think that kind of research is interesting, but feminists are prone to jumping to conclusions.
I'm afraid researchers in general are far to prone to jumping to conclusions.
> As soon as they see any data that can be interpreted to support the presence of discrimination, the case is closed and no further inquiry is being made.
That's not my experience with such research. On the contrary, there are usually a progression: first look at the statistical data to see if there appear to be differences, and if there are, then try and find out more about those differences, why they are there and if they can and/or should be mitigated.
A lot of the work in classrooms, for instance, first started with documenting classroom settings on video, looking at the amount of time spent with various students and how often one or another group was picked to answer questions etc. This work revealed rather stark differences, much to the surprise of teachers who subjectively thought themselves to not do any sort of differentiation.
Now, explaining those differences is indeed complex. And while I don't think there is any support for the idea that boys are dumber than girls (or vice versa) -- there are indeed studies suggesting that young boys have a harder time learning and concentrating in a quiet "at-the-desk" classroom setting. This then has implications for how one should organize class; in general you don't want noisy students to distract those that are more quiet/more mature -- nor might you want to segregate the classroom too much.
> For example, in the wage gap discussion, I have never seen anybody ask an employer why they pay women less. Who knows, there might be some surprising answers.
That amounts to asking employers why they are breaking the law, which makes it a little tricky. In general there are three important questions here: do women earn the same as men (no); are women paid the same amount for the same work as men (no, but the difference is smaller -- especially now than in the 60s); And: Why?
The answer to why is also a two-part answer: partly women do more of the work that is considered free (or very low wage when people are hired to do it): housework and staying at home with children. Additionally, due to women being overrepresented in careers with lower wages, in a typical family, it makes more economic sense for the woman to stay home with young (and/or sick) children -- which again means the woman might progress slower in her career.
To cut an already too long comment short, have a look at for example:
http://www.businessweek.com/articles/2012-06-21/equal-pay-pl...
http://thinkprogress.org/economy/2013/04/09/1839281/on-equal...