The CEO’s office is not the only leadership question mark at the Atlanta Housing Authority. The agency’s board of commissioners has been in the headlines as well.

Late last year, an investigation of two Atlanta Housing Authority commissioners determined that they made hostile and offensive comments to agency employees, according to an 18-page report that a local law firm representing the agency sent to Mayor Kasim Reed.

According to the report, the agency could be held liable for possible violations of state and federal law because of racially derogatory and sexually charged comments that AHA employees allege were made by commissioners James Allen Jr. and Wayne Jones. Both men were appointed by Reed. Allen continues to sit on the board; Jones died in April.

In emails to board members earlier this year, AHA chief executive Renee Glover warned that conflicts between the board and housing staff were hurting morale.

“The ongoing instability and these types of conflicts continue to erode the confidence of the employees that they will be allowed to do their jobs without the board second-guessing and questioning their professionalism and/or integrity,” Glover wrote on Sept. 20.

Reed has appointed a new member to the AHA’s board: Loretta Young Walker, chief human resources officer at Turner Broadcasting. Reed said he plans to announce two more board appointments by the end of the year, bringing the board of commissioners up to full strength after a long period of partial staffing.

The longtime chief of the Atlanta Housing Authority and the board that governs that agency were close to reaching an agreement this summer that called for her to give up the job she’s held for 18 years, but negotiations have since stalled, leaving the agency in a state of limbo.

It’s not clear why the severance agreement and transition plan went no further. But, in internal documents, AHA leader Renee Glover argued that a “lack of follow-through” has created uncertainty across the sprawling agency. At some point, the agency — which has a budget of roughly $265 million and provides services to tens of thousands of families — will start losing its top performers, Glover warned.

The delay is hurting the agency and its employees, Glover wrote in a Sept. 20 email to Daniel Halpern, the chairman of the authority’s board, and Cecil Phillips, Halpern’s predecessor.

“The instability and uncertainty hang like a storm cloud over the agency,” she wrote.

Under the proposed deal, Glover would have received about $400,000 — the equivalent of 15 months pay, according to documents obtained by Channel 2 Action News and The Atlanta Journal-Constitution through open records requests.

Glover’s personal attorney, Michael E. Kramer of Buckley & Klein, told the AJC a deal was put in writing in mid-July after extended negotiations involving the chairman of the AHA’s Board of Commissioners and the board’s outside attorneys.

The deal “was subject to and pending the board’s approval, but we understood the deal would be presented to the board — and then we’ve heard nothing back from them,” Kramer said in an emailed statement. “And that’s where it stands.”

Glover, who came to the AHA in 1994 during a period of tumult, reaped national acclaim for her work in tearing down some of the city’s most squalid public housing projects and replacing them with mixed-income developments, a strategy that became known as the “Atlanta model.”

The Atlanta Housing Authority is now the co-developer of 16 master-planned, mixed-income communities. The agency administers subsidies for rents at more than 70 privately-owned housing communities. It serves about 50,000 people, receiving about 80 percent of its money from the federal government. Most of the remainder comes from real estate transactions and investments.

Conflict between Glover and Mayor Kasim Reed boiled over in October 2011, when Glover announced in a press release that Reed’s appointees on the housing board had made it clear they wanted to hire a new CEO. She said she intended to negotiate an exit.

At the time, she was less than two years into a five-year contract with a $325,000 annual salary, not counting other benefits.

After Glover went public with her stance, Reed fired back. The first-term mayor said last year that his trouble with Glover started when a board appointed by previous mayors — which he described as a “lame duck” — awarded her a new five-year contract. That contract took effect before Reed had an opportunity to make appointments to the AHA’s board.

Reed took that as an attempt to avoid his process for opening up various agencies for new leadership. The Atlanta mayor has the authority to appoint members of the agency’s board but no direct authority to hire its CEO.

The rhetoric has since calmed down, at least in public. On Monday, Reed said he is “comfortable with the leadership at AHA through the end of the contract.” He said he had hesitations about a severance package that could cost about half a million dollars.

Reed said that, from his perspective, the AHA is stable.

“I’m comfortable with whatever the board wants to do,” said Reed, who has selected four of the six current board members. The board includes executives from businesses and non-profits.

The agency faces several challenges along with questions about its leadership. Magnolia Park, an AHA-sponsored mixed-used community, is in “severe financial distress” and faces foreclosure proceedings, according to one document. Meanwhile, more than half of the AHA’s clients are not compliant with the agency’s work requirement, according to a presentation for the board in early October.

Back in September, Glover warned key board members that the AHA was beset by uncertainty and dysfunctional relationships between some board members and staff. After several board meetings where commissioners grilled staffers, she said, she had to remind employees to stay focused.

Both Halpern and Glover declined to comment Monday.

“I’m going to defer to the board’s independence,” Reed said of the breakdown in negotiations between Glover and the board. “For me, there’s no urgency around this. I’m not going to spend any energy on it.”