Gender discrimination is gender discrimination. It doesn't matter if it's a female directing discrimination against a male or vise versa. The laws work equally for both sexes. It's also possible to have gender based discrimination in same sex situations if one or both of the employees are homosexual.
There really isn't enforcement per se with these laws or most civil rights laws. These laws just give employees a means of redress when and if they are discriminated against. In theory, an employer could continue to discriminate against employees indefinitely and there's very little the EEOC or civil courts can do other than levy penalties for non-compliance, and even then only if the employees file EEO complaints or federal lawsuits. Neither the EEOC or civil courts can order any employer to fire any employee for discrimination.
As far as the validity of the suit goes, I have no way of gauging that without hearing all of the story, and it appears as if we're only getting half of it. But let's say everything in the story is true. Initially it would be pretty hard for them to make a case. Even if a manager moved employees offices to the bathroom, that in and of itself would be a pretty weak case for sexual discrimination. Just because your boss is an asshole, doesn't mean they are doing anything illegal. However, if it's true that management launched investigations against the employees because they filed an EEO complaint, that would be a pretty serious charge against the agency. It's called reprisal, and it's illegal under the law. Even if the original complaint had no validity, they still may have grounds for a reprisal case. As far as reprisal cases go, administrative law judges in EEOC tend to favor complainants as far as the standards for evidence goes. If the employees had clean employment records previously, and after filing an EEO complaint they are getting investigated, the agency is going to have some serious explaining to do.
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