The Department of Labor's Office of Federal Contract Compliance Programs found that Savannah River Nuclear Solutions discriminated against female and black employees in pay from 2009 through 2010. The company denies this but has a conciliatory agreement to compensate these employees.
This sounds like one of those situations where it is cheaper to settle out of court. The settlement is for $235,000 across 72 employees. That is only $3263.89 per employee. Considering these are STEM jobs and probably pay well this discrepancy is probably fairly small percentage wise and easy to not notice.
In addition the article mentions the company had a $2.5 billion contract in 2009. That makes this amount incredibly small in terms of bookkeeping.
Breaking down these numbers start to look statistically insignificant. This is looking like the government trying to force exactly equal outcomes and assuming small discrepancies are discrimination.
Please note that the article does not give any indication of the incomes of any of the employees or their job specifications other than being STEM jobs. I can only assume the STEM job is fairly decent pay perhaps above $70,000 a year.