When thousands of passengers were stranded or delayed at the height of this winter's storms, Keolis, the French company that operates the MBTA commuter rail, blamed the weather.
But even now — without a flake of snow on the ground — the rail operator is struggling to provide trains that run on time and with the necessary number of seats.
Back in February, about 67 percent of trains ran late, and Keolis pointed its finger at the exceedingly harsh winter. But in May about 14 percent still ran late. And, to commuters' dismay, the May 2015 performance was worse than the previous year, when the Massachusetts Bay Commuter Railroad Co. was running the system.
The news does not get better: As summer approaches, Keolis is warning customers that one line may face even more delays — this time because of the heat.
It is not just a lack of punctuality that is bothering commuters. Longtime riders say they have endured standing-room-only rides during their commutes, a result of trains with fewer passenger cars than normal.
The company has said it usually needs at least 356 coaches for all of its trains to run at regular capacity. But Keolis has fallen behind on getting enough coaches ready: On June 1, the company had only 339 coaches available for the commute that day, according to the MBTA.
It's wearing out the patience of commuters who, after a winter of crowded and delayed trains, are still standing in the aisles or calling baby sitters to say they're going to be late.
"I feel like I'm in the Dark Ages on these trains," said John Carulli, of Southborough, as he stood in the aisle of the 5 p.m. Framingham/Worcester Line train out of South Station last week. "I haven't sat down in this train for a year."
Keolis took over the commuter rail in July, after beating out the longtime operator, Massachusetts Bay Commuter Railroad, for a $2.68 billion, eight-year contract.
Within months, a combination of extreme weather, leadership failures, and aging trains and tracks swept up the company into a perfect storm of perpetual problems.
Thomas Murray, the president of the local chapter of the Transport Workers Union, said crews normally start inspecting and repairing air conditioning units during the winter. But this year's snowstorms delayed that schedule, and workers are now scrambling to make sure the units work.
"We know this is frustrating to our passengers and we want them to know that we're working to put capacity back into the system as rapidly as possible," said Keolis spokeswoman Leslie Aun.
Aun said the continuing problems have mostly affected lines that run from South Station, particularly the Framingham/Worcester and Franklin lines. By the end of the week, the company plans to add more coaches to those lines, she said.
Fewer trains are running on time under Keolis management than they were last year, when Mass. Bay was in charge: About 82 percent of trains arrived on time in April, compared with 93 percent last year. About 86 percent arrived on time in May, compared with 89 percent last year, according to a review of statistics from the T.
Those delays cost Keolis money. Under its contract with the T, Keolis can be fined up to $434,425 a month for late and canceled trains. The company has had to pay that maximum penalty in each month since October, the first time the fines were assessed.
Some of the delays aren't unique to Keolis. On the Framingham/Worcester Line, for example, the company struggles with a problem that dogged the previous operator. The tracks, formerly owned and maintained by private railroad company CSX, are old and expand with the heat, which can make them buckle. During hot weather, trains must slow down to 30 miles per hour to avoid going off the rails. The commute time for some trains can nearly double on hot days.
Keolis has had to make do with the fleet of aging locomotives provided by the MBTA, some of which have been in service since 1974.
Keolis officials were counting on 40 new locomotives when they took over, but many of those had to be repaired as soon as they got to Boston, the Globe reported in January. Murray, the union president, in March referred to the new locomotives as "junk" when he testified in front of the Legislature.
Only 23 of the 40 locomotives are in service. But because the locomotives have components that are new, complex, and unfamiliar to employees, required inspections are taking longer, according to T spokesman Joe Pesaturo.
In some cases, the older power cables that connect the locomotive to the coaches caused electrical problems that workers were encountering "several times a week," Pesaturo said.
"With such complex vehicles, some early issues and faults are expected as the vehicles transition into daily service," Pesaturo wrote in an e-mail. "Procuring a state-of-the-art locomotive is not like going to a car dealership and driving a new vehicle off the lot."
During the height of the winter storms, the agency sought to address the problem by leasing extra locomotives. One of the leased trains went into service on Monday, according to Pesaturo.
But Keolis's problems stretch well beyond trains and cables. Beverly Scott, the T's now-former general manager, also believed absent leadership exacerbated the problems caused by the winter weather.
In a batch of e-mails released by the T last week, she told one of the commuter rail operator's highest officials that top leadership was "missing in action" during the debilitating winter storms.
Even now, the company is operating without a chief mechanical officer, nearly nine months after David Plumb stepped down. Aun said the company hopes to hire a permanent replacement by the end of the month.
Joseph A. English, who heads the local chapter of the Association of Railroad and Airline Supervisors union, said the chief mechanical officer "is the guy who tells you what needs to be done first, second, and third."
The chief mechanical officer plays a crucial part in making sure the trains are running — especially with an aging fleet. Every year, the trains and tracks become less and less resilient — and the beating from this winter has not helped.
Keolis replaced its first general manager, Thomas Mulligan, with his deputy, Gerald Francis, but English still believes the company needs its leadership to "step up."
Murray also said workers are struggling with those in charge.
"There's a disconnect between the people that they brought in from France and the midlevel managers," said Murray. "And there's a disconnect between the MBTA and Keolis itself."
Nicole Dungca can be reached at email@example.com. Follow her on Twitter @ndungca.