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He was elected on a promise of astute management and fiscal prowess, and on a bitterly cold night in January 2016, Governor Charlie Baker touted his work.

State officials had “tightened our belts” financially, he told the House chamber. The MBTA, paralyzed the winter before, was working to double the capital investments into its decrepit infrastructure. The customer-friendly Registry of Motor Vehicles he promised was moving toward reality. “And we are just getting started,” Baker said to applause in his first State of the Commonwealth speech.

But those public-facing agencies that helped buttress Baker’s reputation as a governmental manager, and whose turnaround efforts he spoke of that night, are now wrestling with something else, experts say: management problems.

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A series of reports examining the MBTA and Registry have thrown a harsh light not just on the long-turbulent agencies, some of whose problems date back decades, but also on the prescriptions pushed by Baker, a technocrat who has long emphasized the blocking-and-tackling of state government.

Wait times have dramatically improved at the Registry, as Baker promised, with 87 percent of customers waiting 30 minutes or less. But the push to get there may have come at a cost, some officials charged. Internal auditors said the intense drive to slash the long lines at Registry branches drew attention away from critical public safety work. A state-commissioned firm hired in the aftermath of a fatal crash that exposed failures in the agency also said that staff felt customer service was prioritized above other, behind-the-scenes operations.

Baker’s calls to tighten the MBTA’s spending, while expanding its capital budget, also found success, elevating capital spending to more than $1 billion last year. But that emphasis has been “detrimental” to the day-to-day operations, a T-hired panel found, and many times, it said “financial considerations take precedence over operational performance and safety.”

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The findings and the parallels between the agencies’ shortcomings, critics say, open questions of whether Baker’s solutions were too narrowly tailored for such complex departments. It’s a contention the second-term Republican denies.

“I think the way you fix the forest is one tree at a time,” Baker told the Globe. “There’s a lot of people who over the years have said a lot of things about what they were going to do to improve service and invest in the MBTA and improve service at the Registry — and they didn’t do it.”

In the eyes of his critics, there is some irony that a raft of management problems now confronts Baker, the former health care executive who ran for the office offering an antidote to what he called “significant management failures” under his predecessor, Deval Patrick.

“It certainly takes the shine off,” said Michael Widmer, former president of the business-backed Massachusetts Taxpayers Foundation, who has argued that Baker miscalculated the culture of the T and Registry. “He’s a problem-solver by nature. But his focus on particular problems within an agency is different than fixing the agency.

“You have a governor who’s committed to taking on these challenges,” Widmer added, “but here we are five years in and what do we have to show for it? It’s certainly disappointing.”

State Senator Eric P. Lesser, a Longmeadow Democrat who emphasized the “tipping point” facing the state’s transportation networks, was more blunt: “To put it plainly, in 2014 he campaigned as Mr. Fix-it. And there’s quite a lot that isn’t fixed.”

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To be sure, Baker has made headway on an array of priorities. His administration resurrected the state’s Health Connector, where sign-ups for insurance coverage have surged. The Department of Children and Families, which Baker as a candidate called “broken,” has beefed up its staff and policies amid an ongoing struggle to correct systemic gaps.

Baker, a former state budget secretary, has also presided over back-to-back $1 billion budget surpluses, after the state faced yawning deficits early in his first term.

“You want me to go down all the other things we fixed since we got here?” Baker said in a Globe interview.

At the T and the Registry, Baker’s initial priorities were shared, if not cheered, by those who have been stranded on a broken-down train or stuck in line at the Registry. And both agencies, experts say, have suffered from deep-seated neglect from previous policy-makers.

With the T, Baker faced little choice but to take action. The historic winter of 2015 crippled the system, and commuters quickly screamed for change. Baker signed into law a new oversight board and installed leaders who pumped millions of dollars into “winter resiliency” while working to, as Baker puts it, “get its fiscal house in order.”

Stephen J. Silveira, a lobbyist and a former chairman of a state transportation finance commission, said making meaningful improvements to the T generally takes longer than a political cycle or gubernatorial term, which has made it easy for others to dodge responsibility.

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“The political thing to do, going back from the beginning, was to avoid the T or push it onto someone else,” said Silveira, whom Baker appointed last year to a commission that studied the state’s future transportation needs. “I don’t think it’s a reflection of him as a manager at all. To his credit and the administration’s credit, they took it on.”

Baker has said he recognizes that the T remains a work in progress.

“The governor’s committed to improving the T. The governor is committed to safety,” said Ray LaHood, the former US transportation secretary who was part of the panel that produced the 69-page safety report on the agency, this month. “That’s the kind of political leadership you need if you’re going to improve transit.”

Baker’s office also rejects the premise that its approach played a role in the Registry’s now well-documented failures. Indeed, the outside firm hired to review the agency, Grant Thornton, found the RMV agency had a policy spanning “multiple administrations” of not prioritizing warnings sent from other states about dangerous Massachusetts drivers.

A June crash in New Hampshire that killed seven people, allegedly caused by a West Springfield man whose license should have been stripped, exposed the problem. But Baker aides argue it had never siphoned staff or money from the unit responsible for processing the alerts to help in service centers.

“If we’d known about it, we would have done something about it. I feel terrible that we didn’t know about it,” Baker said of the backlog of alerts that officials discovered dating back years. “Once we did, in four weeks, we cleaned up the whole backlog” of major violations.

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Nevertheless, the one-two punch of problems has invited a level of scrutiny of his administration unseen in his first term.

The Legislature’s transportation committee held an hourslong oversight hearing in July digging into the Registry, and the withering report on the MBTA’s safety failures has supercharged calls to create new tax revenue to funnel into the agency, a move Baker has opposed.

Baker and Democratic lawmakers have also squabbled over his request for $50 million to go toward capital projects, conduct inspections, and improve maintenance at the T — efforts he said would also address safety. Legislative leaders ultimately sliced it to $32 million, and House Speaker Robert A. DeLeo suggested Baker provided muddled reasons for the cash.

“The common thing here is what I would call a management issue: the danger of missing key issues by focusing on one or a limited number,” said Representative William Straus, the House chair of the Joint Committee on Transportation, of the Registry and MBTA. “You can’t look at these and think that these were rogue agencies misperforming on their own.”

The findings have caused even those who have long supported efforts to address the MBTA’s multibillion-dollar backlog of repairs to point out the approach’s shortcomings.

“I’m not debating that [capital spending] wasn’t a priority,” said Richard A. Dimino, president of the business group A Better City, “as I’m not debating that customer service [at the Registry] wasn’t a priority and needed to be improved. The governor, by leaning in, it’s something he should get credit for.

“But it’s not one or the other,” he said. “You have to be able to do a number of things at the same time.”

If there’s been political fallout from the problems, however, it’s unclear to what degree. Baker has long remained the country’s most popular governor, according to quarterly Morning Consult polls, the last of which showed his approval rating holding at 73 percent between July and September. The most recent reading came directly after the Registry fell into turmoil and a Red Line train derailed, disrupting service for months.

That it didn’t chip away at Baker’s public profile is, in some ways, “astonishing,” said Stonehill College political scientist Peter Ubertaccio.

“He attacked his predecessor on his management of state government and he’s had some similar management issues with state government. But it hasn’t had the same kind of impact on his political standing,” Ubertaccio said. “It’s a bit of a puzzle.”


Matt Stout can be reached at matt.stout@globe.com. Follow him on Twitter @mattpstout