“Companies and employers who do good things have discrimination claims filed against them and it doesn’t distract from the respective missions of those companies because it doesn’t mean they discriminated,” Gil A. Abramson, a lawyer who represented the center in the labor dispute, said in an interview.

The center, he said in a subsequent statement, “wishes all of our former employees the best in their future pursuits.”

The settlement is the latest unexpected twist in the case of Mr. Birkenfeld, who served 31 months in prison after pleading guilty for his role in a tax evasion scheme despite having blown the whistle on UBS. It also put the whistle-blower center, a group accustomed to shining a spotlight on problems elsewhere, in a rare position: on the defensive.

Even so, the employment dispute does not appear to have slowed Mr. Kohn, who remains a visible force testifying before Congress and representing whistle-blowers from inside the government and across the corporate world. His cases have involved the 1995 Oklahoma City bombing and no-bid contracts in Iraq. Just recently, a publicist emailed the news media to promote Mr. Kohn as an expert about a sharp rise in whistle-blower tips to the Securities and Exchange Commission.

The center’s dispute with Ms. Williams and Mr. Renner surfaced soon after the Internal Revenue Service announced the $104 million award to Mr. Birkenfeld in September 2012.

Days later, Mr. Renner and Ms. Williams attended a staff meeting with long-term employees from the center and from Kohn, Kohn & Colapinto, the related law firm that handled Mr. Birkenfeld’s case. At the meeting, Ms. Williams and Mr. Renner said, the firm’s partners discussed possible bonuses and raises for some of the employees, some of whom were paid less than $60,000 at the time.

The bonuses arrived soon after, but not the raises, a decision that was attributed to funding problems. The partners would not disclose the amount the firm received in the Birkenfeld case, Mr. Renner said, but “they claimed it was not as much as we might think.”