Under the terms of his contract, Burns, who ran the agency until 2005, was eligible for an annual $3,000 bonus for meeting on-time performance goals.
He earned the first such bonus in 2001, according to Muni spokeswoman Kristen Holland. That is the same year Muni began inflating its performance rates, according to Muni's Chief Information Officer Travis Fox.
Burns earned his second and last $3,000 bonus for meeting on-time goals in 2002. Under his watch, Muni's on-time performance increased from 55 percent in 2001 to 71 percent in 2005, according to the agency's inflated data.
Burns received a total of about $30,000 in bonuses for meeting other goals during his tenure. He wrote in an email that he recalled accepting some of those bonuses but said he turned down the additional money when the agency's budget was tight.
Ford, Muni's CEO from 2006 to 2011, was eligible for bonuses worth 10 percent of his base salary, or about $31,000 each year. He had the highest salary on the city's payroll, earning $308,000 annually, and he received bonuses for three of his five years at the transit agency.
Although he received a total of about $69,000 in bonuses, most of the money was not tied directly to meeting or improving Muni's on-time performance. One-quarter of his annual bonus was based on 10 factors; improvements to the on-time rate represented one of those factors.
During Ford's tenure, the on-time rate improved from 69 percent to 73 percent, according to Muni's inflated figures. A percentage of the bonuses he received were based on that improvement, according to Paul Rose, spokesman for the San Francisco Municipal Transportation Agency.
"I believe the board may have recognized my performance regarding on-time performance from one year to the next to note the progress I made," Ford wrote in an email to The Bay Citizen.
In a 2010 memo sent to Ford and other top Muni managers, Fox, the chief information officer, outlined accounting maneuvers that he said resulted in on-time rates that were 13 to 18 percent higher than the actual rates. Those maneuvers, which Fox called "quirks," included not counting inbound trains headed to the Embarcadero station; expanding the definition of “on time” from 1 minute early or 4 minutes late to 1 minute early or 4 minutes and 59 seconds late; and excluding buses that skipped their routes.
Ford said he didn’t remember seeing the memo, adding that it would have set off “alarm bells.”
Ford, who is now working as a consultant, said that because those maneuvers were in place before he arrived, the progress Muni made under his tenure was real, based on an "apples to apples" comparison.
Burns, who now runs the Santa Clara Valley Transportation Authority, said he had no knowledge of the maneuvers.
“This is a level of detail that is something I had no reason to question or be involved in,” Burns said. “If I had any indication that 4 minutes and 59 seconds was being used, I would have reported that.”
Muni officials say they have no plans to recoup the bonus money paid to the men.
“The performance bonuses were based on dozens of service metrics, not just on-time performance. We are not going to go backward at this point,” said Tom Nolan, chairman of the SFMTA Board of Directors, in prepared statement. “Moving forward, I am confident that our efforts to craft more comprehensive service standards will give our customers more useful information and help us manage service more effectively.”
Muni has said that beginning this month it will no longer use the accounting "quirks" when reporting its on-time performance rates.
The agency's two previous chief executives, Michael Burns and Nathaniel Ford, received the bonuses. Both men have denied knowing about the on-time rate inflation.