The financial wheels nearly came off the Napa County Transportation and Planning Agency in recent years, with the public and, for a time, agency directors, none the wiser.

The magnitude of the agency’s financial problems surfaced two weeks ago when new managers reported tracking down $2.6 million in federal grants that had been lost or ignored for up to two years.

In 2007, the agency, which runs Napa County’s transit and paratransit services, failed to claim $2 million in federal funds needed to buy new buses for the VINE.

“How can you miss $2 million? I can’t tell you. I wasn’t here,” Tom Roberts, NCTPA’s new manager of planning and programming, said in an interview last week.

The agency expects to regain the entire $2.6 million, enabling it to buy three or more new buses, improve bus stops and upgrade maintenance. Despite past oversights, no money will be lost, Roberts said.

“It’s kind of like a windfall now, isn’t it?” Roberts said. Because of Roberts’ sleuthing, one official at the Metropolitan Transportation Commission dubbed him “the Sherlock Holmes of transit.”

Recent years were hard ones for the agency, which lost senior managers and for two years had an executive director with no transportation background.

“We got a sense a year or two ago that things weren’t what they should have been,” said Jim Krider, the Napa city councilman who chairs the agency’s board of directors.

When Jim Leddy, a former legislative aide, resigned as executive director in September 2008, the board hired Paul Price, a career transportation manager, who took charge in January.

Price was hired with the mission of making the agency fire on all cylinders, Krider said. The agency pulled back from becoming a countywide environmental and growth management agency, deciding that transportation had to be its first priority, he said.

Pam Kindig, the county auditor/controller who retired earlier this year, said NCTPA’s financial disarray was confirmed when her agency was invited to conduct several audits.

“We were trying to take care of it before it became a huge problem,” Kindig said. “I was trying to avoid a situation that could have been a crisis ... in the media.”

At her recommendation, the agency hired a full-time finance manager, a position that Antonio Onorato assumed only a couple of months ago. Roberts, who ran transportation systems in Santa Barbara for 20 years, became the agency’s first full-time planning manager. Price charged Diana Vargas, his deputy director, with holding managers accountable.

The agency had lost much of its institutional memory when several key managers and the executive director departed, Roberts said. The agency has fewer than a dozen employees.

The combination of staff turnover and possible “mission creep” resulted in basic financial accounting and planning not getting done, he said.

It was with trepidation that staff told the board last month of the federal grant monies that had been lying fallow or unclaimed.

“Obviously taking this to the board was sensitive. The board needed to know that the staff and the agency are getting it done, yet making it public shows there was a weak spot somewhere,” Roberts said.

Board members, who had been briefed earlier on the findings, voiced appreciation that the new regime was bringing financial order. “History is history,” American Canyon Mayor Leon Garcia said.

“We’re going to see accountability now,” St. Helena Mayor Del Britton said later.

“Transportation financing is very complicated,” Krider said in an interview. “I think the previous executive director did not have the technical skills that Paul does.”

Price said the board was clear about his mission when he was hired last winter. “They said they wanted me to focus on transportation issues. Something isn’t working right.”

Management jobs were reorganized for clearer lines of responsibility and vacancies were filled with people with needed expertise, he said.

Price said he pledged to board members that he would be forthcoming about any shortcomings he discovered. “You have to be transparent. If you hide, you will be pilloried at some point,” he said. “If we have something that needs to be said, let’s get it out and move on.”

Jacques LaRochelle, the city of Napa’s public works director, said he was impressed by Price and his new management team. “The new guys, they really cranked it up,” he said.

Even during the years of disorganization, the agency was run “conservatively” with “decent” financial reserves, Roberts said. What lagged were an assortment of projects, including the purchasing of new buses and construction of park-and-ride lots.

The agency was relying more on state transportation funds, which come with fewer restrictions, than federal grants, Roberts said.

Now that staff is on top of federal grants, it is reviewing all sources of state funding for mistakes or oversights. The board will get an accounting of state funds this fall, Roberts said.

For possibly the first time, the board is now getting financial reports every month, Onorato said. “You’ll see where the money is coming from and where it’s going,” he said.

At the October meeting, Onorato presented the board with a revised budget for 2009-10, updating numbers adopted four months ago. Expenses and revenues were each adjusted by several million dollars.

While these revisions won’t have an impact on transit operations, they capture the agency’s real financial situation, Onorato said.

Professionally speaking, getting the agency squared away has been an exciting time, Onorato said. The future may be less exhilarating.

“We’re going from an agency kind of all over the place to one that is predictable and boring,” he said.