Flores refused to do an on-camera interview with ABC News but in a phone conversation insisted he was not influenced by the group's high level connections and said he chose the program because historically there was not a lot of funding for programs aimed at delinquent girls.
At a recent fundraiser, Elayne Bennett told ABCNews.com that her organization is all about good friendships.
"We're really about positive friendships. And a good, solid friendship is a beautiful thing," she said.
She said of the career Justice Department employees who are now speaking out about their allegations of favoritism: "They say that others are playing politics. But they are doing this because of politics. They don't like the politics of our group and others. That's where that nastiness comes from."
She added: "Inside leaking. You have to be careful of that."
Meanwhile, competing with Best Friends for a federal grant from the OJJDP was a Washington non-profit, the Rape Abuse and Incest National Network (RAINN), an advocacy group for victims of rape and sexual assault.
Among other things, RAINN runs a telephone hotline for victims of rape and sexual assault, which has put hundreds of thousands of victims together with local rape crisis centers. In the category of OJJDP grants for which both organizations applied, Best Friends ranked 51st, while RAINN came in at 14th. RAINN did not receive a grant from the OJJDP.
A spokesman for RAINN declined to comment for the story. Meanwhile, others in the juvenile justice arena continue to question why Flores would ignore the advice of his own staffers and award grants to lower-ranked organizations.
"Under Flores, his office has abandoned its core mission in favor of peripheral issues with ineffective programs," William Treanor, executive director of the American Youth Work Center, told ABCNews.com.
"The office has abdicated respect and leadership in the juvenile justice field," he said. The newspaper published by Treanor's organization, Youth Today, first reported the controversy over Flores' grant awards.
Although OJJDP administrators have some discretion under the law to award grants to whomever they want, Flores is still required to get approval for the awards from his superior.
But because of Best Friends' lower ranking, 53rd out of 104 grant applicants considered, his superiors might have overruled him, if they knew of the group's poor standing, according to Justice Department officials involved in the process.
To make sure that a grant to Best Friends was approved, officials say, Flores simply created an entirely whole new category which the organization's grant proposal would be considered.
The category, Flores wrote in a memo to then-Assistant Attorney General Regina Schofield, who oversaw the awarding of Justice Department contracts and grants was for grantees "utilizing school based outreach efforts directed at preventing high-risk activity (out-of-wedlock pregnancy)."
Flores went on to write Schofield regarding Best Friend's proposal: "This application has the highest score that met the criteria under the administrator's priority area."
What Flores left out of the memo was that Best Friends had the highest score because by manipulating the categories, Best Friends was the only organization that qualified at all in that particular category.