CHICAGO — Workin’ on the railroad turned out to be very lucrative for former Metra deputy executive director G. Richard Tidwell.

Last year, even as budget worries prompted Metra to raise one-way fares by 6 percent and to add $2 to the price of a weekend pass, Tidwell took home nearly $1.25 million in salary, bonuses and benefits from the commuter rail agency, records show.

The bulk of that — $876,634 — came from a little-known deferred-compensation benefit that Tidwell, 61, cashed in when he retired from the agency in March 2009. He also received a “split-dollar” life insurance payout of $290,190 before he retired.

The commuter rail line has faced an unwanted public spotlight in recent months thanks to Philip Pagano, the top Metra boss, who took his own life by stepping into the path of a Metra train May 7 in Crystal Lake in the face of an internal Metra investigation into bonuses and cash advances he had awarded himself.

But the public agency’s generosity didn’t stop with Pagano, according to an analysis of Metra payroll records by the Chicago Sun-Times and the Better Government Association. The examination found that the agency doled out hefty cash payouts for unused sick time and vacation days to Tidwell, who was the agency’s No. 2 executive behind Pagano, and several current management workers, even as it asked riders to dig deeper to pay for their commutes. The one-way and weekend-pass fare hikes that the Metra board approved late last year took effect on Feb. 1 of this year. In 2008, Metra raised fares 10 percent across the board.

Metra officials say they have no reason to believe there has been any impropriety with the payouts to anyone other than Pagano. They also have no evidence that anyone else at Metra is a target of a criminal investigation.

“We have not uncovered any evidence that any other Metra executive engaged in any conduct warranting immediate remedial measures,” James G. Sotos, the attorney hired to do Metra’s own investigation of Pagano, said in his report.

But Sotos’ report also revealed an unspecified “inquiry” from the U.S. attorney’s office in Chicago to Metra. Last week, Metra officials acknowledged for the first time that federal authorities have sent them two subpoenas as part of a criminal investigation. They would not immediately release those subpoenas, and spokeswoman Judy Pardonnet said she had no details about them.

Tidwell and several current Metra managers benefitted from Pagano’s authorizing vacation and sick-day buyouts, according to records obtained by the Sun-Times and the BGA. Pagano authorized a total of $224,157 in payouts to Metra employees in 2009, $428,182 in 2008, and $25,422 in 2007.

About half of the $677,761 in buyout money during that three-year period went to Pagano himself and to Tidwell, with Pagano getting $232,761 and Tidwell $114,945.

Thirty-four other Metra employees got vacation and/or sick-day buyouts last year, the biggest of those totaling $22,220.

Metra’s board has now banned any further such payouts, noting that Metra rules should have kept Pagano from handing out most, if not all, of them to begin with.

“It is painful for us to look at decisions where [Pagano] rewarded other managers in a way that was not consistent with [Metra] policies or procedures, or the understanding of the board,” board Chairwoman

Carole Doris said Friday. “It is a management issue we are addressing.”

The Sun-Times/BGA examination also found that:

••Despite the down economy, 151 unionized and nonunion Metra employees each made more than $100,000 in 2009. That doesn’t include retirement contributions and health-benefit costs. Factoring those in, 524 employees — 18.4 percent of the rail agency’s 2,848-member work force — made $100,000 or more in total compensation last year.

••Metra paid nearly $20 million for overtime last year — amounting to about 11 percent of its nearly $180 million payroll.

••Eleven percent of its employees — a total of 310 — made more than $20,000 apiece in overtime pay in 2009. Nearly a quarter of Metra workers — 685 — were each paid more than $10,000 for overtime.

Pagano was in line to be paid more than $1.1 million by Metra this year, after making $329,185 in 2009 and $441,280 in 2008.

A week after his death, Metra issued its report on the investigation it hired Sotos to do, concluding that Pagano had violated agency rules “and likely various state and criminal laws” by forging Doris’ signature earlier this year on documents that allowed him to get two vacation bonuses totaling $114,072.

Tidwell, who is now living in Arizona and who did not return phone calls seeking comment, actually was paid more than Pagano last year. That was thanks to incentives that Metra board members set up for him and Pagano about 20 years ago. Those deals guaranteed hefty bonuses to Pagano and Tidwell if each stayed with the agency until they turned 60. Both did.

In 2008, Tidwell’s base salary had been $235,081. But he boosted his pay that year by 50 percent, to $352,193, in part by trading in some or all of his 10 weeks of vacation time for a cash payment of $49,729, records show. In addition, Metra paid him $28,526 for unused sick days and $16,346 for unused vacation time that dated to before 2008.

On top of that, the agency made a $20,500 contribution to Tidwell’s 401(k) retirement plan — part of a series of five-figure 401(k) payments he had been getting every year since at least 2005.

Metra offered the deferred-compensation and life-insurance packages to Pagano and Tidwell in the late 1980s and early 1990s. It’s not clear whether the Metra board discussed them publicly. Federal prosecutors told Metra not to release records involving those incentive plans, according to Pardonnet.

Former Metra board Chairman Jeffrey Ladd, who helped create the compensation packages for Pagano and Tidwell, could not be reached for comment.

Sotos noted in his report that the deals were designed to “ensure continuity at the highest management level.” But he also suggested the packages were kept hush-hush.

“Even if appropriate, it is important that agreements such as these be transparent so that public debate may occur on the feasibility of these agreements in the same way the public debate on the size of public pensions is presently ongoing,” Sotos wrote.

In light of the allegations of wrongdoing by Pagano, Metra has begun reviewing its pay policy. Its board has formed two committees to review “executive compensation and benefits as well as compensation and benefits of staff at all levels,” Pardonnet said.

As with other railroads, Metra appears to be somewhat limited in its ability to change wage and overtime scales for its 2,300 union workers because the legislation that created the agency in 1983 required it to adopt freight railroad union work rules.

Even so, “when overtime pay is this pervasive, the taxpayer deserves analysis to prove its cost-effectiveness,” said Joseph Schwie-terman, a DePaul professor who studies the economics of urban transportation. “This has quietly become a huge portion of the agency’s expenses. In the midst of a budget crisis, it needs attention.”

Schwieterman said these new revelations about hefty pay and buyouts for Metra bosses threaten to shake the public’s confidence in the rail system. “When outlays for unused sick and vacation days become this large, something seems wrong,” he said.

Jim LaBelle, a Metra board member, said the agency is determined to make sure it isn’t wasting money. “The things that are being uncovered are things that we need to address,” he said. “We have our work to do, to not only ensure that the trains are running on time, but that we’re spending our riders’ fares in the best way possible.”

Doris said that, despite the cloud over the agency involving Pagano, Metra performs well, carrying 300,000 passengers a day with a 96 percent on-time arrival rate.

“Metra has closed a budget gap in the last year of about $64 million due to poor sales-tax revenues and the basic state of the economy,” she said.

“These are serious amounts of money” spent on salaries and bonuses, she added, “and no one takes them more seriously than me and the board. But, in the context of the challenges we’ve had . . . and still keeping the trains running, we have really shown there is good policy at Metra.”

>> Read the partner story in the Chicago Sun-Times.