The biggest factor in the general economy seems to be work flexibility requirements. For reasons I won't go into here, women tend to demand a greater amount of flexibility from employers regarding things like working hours, travel, and the duration and intensity of high-demand projects. The ability and willingness to prioritize company demands over personal demands tends to pay a premium in the marketplace and is often reflected in who applies for and gets chosen for different positions. In the general marketplace, this means there is a population of people who take lower wages in exchange for flexibility either lower wages in the same field or different positions which pay less.
If we apply a similar pattern to programming jobs, we can explain quite a bit. It seems plausible that programming positions tend to have high demands in this area, selecting out a great many people from even participating. There would be a diversity, however, of positions, with some companies offering this flexibility, but with a larger applicant pool, these employers could pay less money. If women are disproportionately represented in the high-flexibility market, they would find themselves fighting for fewer positions at lower wages compared to low-flexibility workers.