"To do that requires being assertive, taking initiative, probably taking out your list of accomplishments and thereby self-promoting," said Laura Kray, a professor of leadership at the University of California at Berkeley's Haas School of Business. "It turns out people don't like it when women do this."
Kray said both male and female supervisors can have these negative feelings about women when they ask for more money. And that can hold back women's careers—either because they don't get as much money, or because they do but they endure the repercussions of not being very well-liked.
It's not that women don't want more money. A survey of employees, released last year by the human resources trade group Society for Human Resource Management, found that 60 percent of both men and women see pay as very important to job satisfaction.
And yet, researchers have found the gap between men's and women's earnings can start as early as the first paycheck, even when controlling for factors such as choice of job and college major. Generally, other government data show that the gap largely widens as women get older.
Many studies also have shown that women are less likely to ask for more money. One recent survey, released by Elle magazine last summer, found that 53 percent of women had never asked for a raise, compared with just 40 percent of men.
Shirley Davis, vice president of diversity and inclusion at the Society for Human Resource Management, said some women don't even think they can ask for more money when they are offered a job. While men are more likely to see a salary offer as a starting bid, she said women are more likely to think they have to take that offer or turn down the job.
Davis said women also tend to be less likely to tout their own accomplishments on a regular basis, in staff meetings or one-on-one. Those reminders can prime the pump for asking for a raise later.
"We tend to think that our results will speak for themselves and we shouldn't speak up," she said.
The negative reception that some women face when they ask for a raise may seem surprising in an age when many women work, and people like Yahoo CEO Marissa Mayer and former Secretary of State Hillary Clinton are in very powerful, visible leadership roles.
Neale said she thinks it is largely subconscious, and most bosses probably don't even know that they are judging women more harshly.
"We're sort of in second-generation bias now," she said.
That also makes it a complicated issue for women to navigate.
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When Neale is negotiating, she said she's found that she is more successful if she asks for a package of resources that will help make her employer better—rather than just more money for herself.
In academia, she said, that may mean she also shows how more resources for her research, plus additional teaching assistants, will help the university meet its goal of producing more high-profile results.
"Then I'm not getting greedy," she said. "I'm doing things that help the organization."
Kray said there are "accommodation tactics" women can use to handle their own salary negotiations without raising such negative perceptions. These, she said, are "compromises that women can make in the short term to navigate this tricky minefield."
For example, her research has shown that using charm— which she defines as a mixture of friendliness and flirtation—can mitigate some of the negative perceptions women are at risk for when they ask for something like a raise.
But, she noted, those accommodation tactics are separate from what she hopes is a broader conversation about overcoming those negative perceptions in the first place.
In her leadership classes, Kray said the most gratifying feedback she gets is that her class made a student rethink his or her response to a woman in those types of negotiations.
"They say, 'You know what, since then I really think a little bit differently about those knee-jerk reactions I have and I ask myself, 'Would I be responding the same way if (this) were a man?'" she said.
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—By CNBC's Allison Linn. Follow her on Twitter @allisondlinn and Google, or send her an email.