From the article cited:

Interviews with current and former members of the administration, both men and women, suggested that there was no single reason for the gender discrepancy in administration appointments, and several repeatedly spoke of the administration's internal commitment to diversity and gender equity.

But several said that the "pipeline" of candidates appeared to be one problem. They said it seemed that more men than women were put forward or put their names forward for jobs. In part, that might be a result of the persistence of historical discrepancies: men have traditionally dominated government fields like finance, security and defense.

The Obama administration has helped reverse that trend by putting women in top policy-making jobs in traditionally male-dominated fields, officials said. "It makes a huge difference when you have women who are leaders," said Celeste A. Wallander, who was a deputy assistant defense secretary until July. "They tend to have networks of excellent women they can call on."