Three years after becoming Charlotte’s top transit official, Carolyn Flowers’ position as a finalist for a similar job in Jacksonville, Fla., has surprised some elected officials locally.

The Jacksonville Transportation Authority has five finalists to become its next executive director, including Flowers, who came to the Charlotte Area Transit System from the Los Angeles County Metropolitan Transit Authority in early 2010.

City officials are surprised in part because Jacksonville’s transit system is significantly smaller than Charlotte’s, and the area has no firm plans to build any rail transit.

Some speculate that the governing structure of CATS makes running the transit system difficult, with two different governing bodies pulling the chief executive in different directions.

The body that makes most CATS decisions is the Metropolitan Transit Commission, which is made of representatives from the city of Charlotte and Mecklenburg County, as well as the other municipalities whose residents also pay the half-cent sales tax for transit.

The MTC’s main priority is to build the light-rail extension to University City, and to then build commuter rail to Lake Norman.

The city of Charlotte, however, owns CATS buses and trains. After building the light-rail extension, there is a push by some council members and civic leaders to build a streetcar through central Charlotte. Charlotte’s capital budget negotiations broke down in June over plans to build a streetcar using property taxes.

Flowers has said CATS won’t use its money to pay for streetcar operating costs, and isn’t an enthusiastic backer of the project.

Charlotte Mayor Anthony Foxx, a streetcar supporter, said last week he was surprised that Flowers is in the running for the Jacksonville job.

He said Flowers has done a good job leading CATS, but said the “push and pull” of pleasing both the MTC and the City Council can be difficult.

He added that “scarcity” of money can make that job even harder. Revenue from the half-cent sales tax that funds much of Charlotte-area transit hasn’t recovered to pre-recession levels.

Earlier this summer, at CATS’ urging, the MTC passed a new policy to allow alcohol ads on buses and trains, a move that could bring the transit system up to $600,000 a year.

But some city officials were upset at the prospect of buses being wrapped in liquor ads, and the City Council urged CATS to reconsider. The alcohol ads have been shelved, for now.

Cornelius Mayor Jeff Tarte is an MTC member and an active booster of the commuter rail line. He said it’s difficult for CATS to try and build several rail lines with limited funds.

“There is a sense that Carolyn is frustrated that things aren’t moving along,” Tarte said.

He said it’s important for CATS to get a chief executive who will be in Charlotte for the long haul.

“We need people with a long-term vision,” Tarte said.

After Ron Tober left CATS in 2007, Keith Parker led the transit system for two years before Flowers was hired. Parker left Charlotte for the top transit job in San Antonio.

Flowers has been successful in advancing the Lynx Blue Line Extension to University City. CATS expects to have official approval from the federal government this fall on building the nearly $1 billion line.

In addition to Flowers, the board that governs the Jacksonville Transportation Authority has picked four other finalists: Stephen Bland, CEO of the Port Authority of Allegheny County in Pittsburgh; Mike Oglesby, general manager of the SunLine Transit Agency in Riverside County in Southern California; Frank Martin, senior vice president of business development for transit and rail with Atkins North America, a design and consulting firm in Clermont, Fla.; and Nathaniel Ford, former executive director of the San Francisco Municipal Transportation Agency.

The board’s selection committee is scheduled to meet Thursday morning to discuss the job.

CATS said last week that Flowers hadn’t yet interviewed for the job. The transit system said she didn’t apply for the position and was instead contacted by a recruiter.

Flowers declined to be interviewed for the article.

In terms of transit systems, Charlotte is much larger than Jacksonville. CATS handles more than 24 million passenger trips on buses and trains, while Jacksonville’s buses carried 11.6 million passenger trips. There are no firm plans to build light-rail or commuter rail in Jacksonville.

But the JTA also builds some highways and bridges, in addition to the Florida Department of Transportation.

The job also pays significantly better than the top transit job in Charlotte. The previous JTA executive director made $287,000. Flowers makes $201,450.

Davidson Mayor John Woods, an MTC member, said he was surprised Flowers is considering the Florida job.

But he said it’s common for other transit systems to look for good people.

“That’s a fact of life,” Woods said. “Carolyn is a professional. She handles her duties very well.”