It comes from the combination of an underlying conception of social change that (normal) progressives have in addition to certain beliefs that modern progressives have about males and females. When you understand both of these then the popularity of gender issues starts to make a lot of sense.

The first factor is the belief among many progressives that the biggest obstacle to social change is basically the lack of will of the people to stand up for the change. When you see people trying to "raise awareness" or "raise consciousness" about an issue like sexual violence, the assumption is that if we could only get people to care more about it then the problem would go away. In other words, sexual violence exists because not enough of society agrees or cares that it shouldn't exist.

The second factor is that many modern progressives believe in a version of the Blank Slate -- the idea that the sexes/genders are psychologically indistinguishable from birth and that differences emerge between them primarily because of socialization and culture.

A similar version of the Blank Slate is probably completely true of the different races and it has played a big role in reducing racism over the last few decades. It's much more common now to view racial differences in society as differences in culture and socialization rather than biology.

The problem is that many differences between the sexes in society (none of which are necessarily bad) are significantly influenced by biological differences between the sexes. On the other hand, many previous differences between the sexes in society were mostly or purely due to socialization and bias.

So as progressives have increasingly called for social change in more and more sectors of society over the last several decades, they've been more and more successful in reducing sexism and dismantling sexist institutions and policies that were based on ideas that men and women were different in ways that they are actually similar or the same. For example, we now know that men and women are equally intelligent on average and equally capable of working most jobs even though in the past people had very different views of women.

Now we're at a point where almost all of society represents an equal playing field for males and females but some progressives (now SJWs) still see that men and women differ in many areas of society, such as wages and representation in science fields. Also, the historical pattern of stereotypical male and female behaviors still remains. Males are still more violent, females still express more emotion, males seek more status and wealth than women, etc.

This is where the first issue comes into play. Since progressives assume that any lack of social change is due to a lack of will in society, they've become more and more obsessed with trying to make gender (these particular issues) bigger and bigger in society until (according to their philosophy) one day it will be such a huge issue that the whole problem will finally be solved. This is also why they've come up with so many radical and paranoid theories (e.g. "hidden barriers" & "structural forces") to explain why men and women continue to be different in particular ways (e.g. job choice) despite the support in society that most people have for gender equality.

They've succeeded in making gender issues a huge focus of progressives, but the problem is, of course, that men and women will never be identical in every way no matter how hard society tries to make them that way.