ABC News reported that another program that was awarded $1.1 million, twice the amount it asked for, promotes abstinence and was ranked 53rd on a list of 104 applicants.
Washington, D.C.-based Best Friends is run by Elayne Bennett, the wife of Bill Bennett, a former Republican cabinet member and now political commentator.
"We're really about positive friendships," she told Nightline at a 2008 charity gala that included many of Washington's GOP elite. "A good, solid friendship is a beautiful thing," she said.
ABC News reported that many top-rated programs were denied federal grants.
A program to help troubled teens in San Diego, Vista, was ranked number two by the staff out of 202 applicants in its category of prevention and intervention but was turned down for a grant to help deal with inner city teen violence in San Diego.
A program designed to train adult guards to deal with teens in custody was denied federal money even though it was ranked by number two out of 104 in its category.
"What Flores did in this situation is he just stomped on the heads of kids who are very much at risk and in trouble in this country," Earl Dunlap, who runs the guard training program for the National Partnership for Juvenile Services, told Nightline.
"He determined what the rules were gonna be and who was gonna play and who was gonna be welcome in his club. And everybody else could take a hike," said Dunlap of Flores.
In a telephone interview with ABC News before the Nightline report, Flores defended his decisions as in the best overall interest of dealing with teen crime.
He said he was never bound by his staff's recommendations and that he made decisions based "on the overall" need in the country.
Berke said Thursday that his client's decisions on the 2007 discretionary awards "were made in accordance with the law, within DOJ rules, and in good faith to address the needs of children who find themselves in the juvenile justice system or at risk of contact with it."
The OIG also found that Flores, by hiring an ex-Colonel Honduran army who at one point had run for president of Honduras, had violated federal acquisition regulations by failing to go through the competitive hiring process required by federal civil servants.
ABC News reported last June that Hector Rene Fonseca, whose Honduran military career spanned three decades, was contracted to work on faith-based and gang issues, according to DOJ staff members. The staffer familiar with Fonseca's contract said Flores invented the job and that no one in the office knew that job was needed until the HR Department was told to hire Fonseca.
The Inspector General's office said Fonseca was paid about $281,000 over a 2 ½-year period, and failed to adequately document the services that he provided pursuant to contract.
ABC News reported that Fonseca attended Church with Flores, according to DOJ staffers, and is married to Deborah Lynne De Moss, a major GOP contributor. Fonseca himself donated $2,000 to President Bush's reelection campaign in 2004, the same year he was hired, and reportedly raised about $50,000 more on behalf of the former president, even though he could not vote in the election.