By Matthew Hirsch and A.C. Thompson

More than six months after a massive embezzlement scheme nearly toppled Haight Ashbury Free Clinics Inc. (HAFCI), the venerable nonprofit institution is still flailing – facing angry employees, a widening criminal investigation, and staggering cash flow problems.

And, remarkably, the clinics, which provide free health care to thousands of San Franciscans, still don't know precisely how much money former chief financial officer Carl Gill actually stole.

The latest revelations emerged March 9 when employees of the clinics confronted their bosses during a highly charged meeting of the organization's board of directors.

HAFCI has been limping along since Gill's arrest last summer on charges that he siphoned more than $773,000 from organization coffers. HAFCI operates on a roughly $14 million annual budget, employing approximately 200 people at about 15 facilities, including a medical clinic and several drug treatment programs.

At the meeting, HAFCI officials admitted they were unable to make payroll Feb. 14. The cash shortage forced chief executive officer Darryl Inaba to hit up a board member, Eric Flowers, for an emergency loan of $160,000. Flowers came through – on less than a day's notice – and in the end people did get paid.

"I do believe HAFCI will survive," Flowers told the Bay Guardian. "Addressing operating losses is obviously our number-one priority."

But at this point, HAFCI workers don't have a lot of confidence in their bosses. "I wish I could believe that the clinics' crisis has been caused entirely by Carl [Gill], but that just does not seem to be the reality," Sarah Thibault, who works in HAFCI's youth program, told the board.

HAFCI is going $100,000 further into the red each month, according to Guinivire Jones, the current CFO. The organization's mission is to provide free health care to the downtrodden and working poor, but these days the clinics are sometimes unable to buy basic supplies.

Through an attorney, Gill has admitted to stealing from HAFCI, but exactly how much he pocketed is unclear. HAFCI's attorney, David Schwartz, said the clinics are unsure of the rip-off's true scale because the books haven't been scrutinized by forensic auditors, a special breed of number crunchers trained to ferret out fraud.

"The organization cannot afford that," Schwartz told the board. "It's extremely expensive."

The matter isn't merely academic: HAFCI is currently trying to get its insurance company to cover the theft, and as you might expect, the insurance firm is looking for a concrete number, not a ballpark figure. But prosecutors now appear to be digging deeper.

"As of a week ago, Darryl [Inaba] received a call from the District Attorney's Office indicating that they wanted to do further investigation into additional bank accounts that may have existed and that the former CFO may have used," Schwartz said.

The D.A.'s Office won't comment on the case.

Prosecutors could question how HAFCI is spending its funds – most of which comes from local and federal public health agencies. Mary Howe, director of HAFCI's youth program and needle exchange, informed the board that she'd written a $17,000 grant for showers and other facilities at HAFCI's center for homeless adolescents. Though the grant money came through and was deposited with HAFCI's front office, the work was never done.

E-mail Matthew Hirsch and A.C. Thompson