Six years after a federal investigation of a deadly Red Line crash exposed Metro’s lax safety culture, last Monday’s electrical meltdown that trapped scores of subway riders on a smoke-filled train suggests a troubling reality: Despite an ongoing $5 billion effort to repair and upgrade the rail system, Metro’s recovery from the 2009 disaster is a long way from complete.

A preliminary report on the smoke incident, released Saturday by D.C. Mayor Muriel E. Bowser’s office, says firefighters in the tunnel near the L’Enfant Plaza Metro station could not clearly communicate by radio with commanders outside because signal-boosting equipment wasn’t working properly. The equipment is maintained by Metro, and fire officials had alerted the transit agency to the problem several days earlier, the report says.

Why the communications problem happened is one of a raft of questions about Metro safety and maintenance that have been raised in the past week. Top agency officials have declined to comment on Monday’s incident, citing an investigation by the National Transportation Safety Board.

Transit experts outside the agency, however, have voiced concerns about many issues, including the number of smoke and fire incidents on Metro property in recent years, not all of which have occurred in tunnels. There were 171 such incidents in the Metrorail system during 2013 and in the first eight months of 2014, according to Metro records.

Another issue involves the fans used to clear smoke from Metro’s tunnels. Transit experts said it was unclear whether the fans near L’Enfant Plaza worked properly Monday. And one Metro official said the agency’s maintenance records on tunnel fans are not current.

A Metro passenger filmed the scene inside the stranded Metro car, in which people can be seen helping and comforting each other. A Yellow Line train abruptly stopped and filled with smoke in a tunnel in downtown Washington on Monday. (Saleh Damiger/YouTube)

Choking passengers, one of whom died, were stuck for at least 35 minutes on a six-car Yellow Line train just south of the L’Enfant Plaza station. Investigators said the train stopped in the tunnel after encountering heavy smoke caused by a severe electrical malfunction involving third-rail power cables.

Safety experts have questioned whether the train operator shut off air ventilation into the train during the crisis to limit how much smoke entered the cars.

Monday’s tunnel ordeal is, in some ways, is more troubling than the 2009 Red Line crash that killed nine people, transit experts said. They noted that Metro has spent hundreds of millions of dollars in recent years to upgrade the rail system’s infrastructure.

“There are more unanswered questions than in 2009,” one longtime Metro official said. Like other transit experts, inside and outside the agency, he spoke on the condition of anonymity because he was not authorized to comment publicly.

After taking charge of Metro in the wake of the Red Line catastrophe, former general manager Richard Sarles — who retired Friday, as long planned — said repeatedly that one of his top priorities was improving the subway’s infrastructure, elevating it to “a state of good repair.” And in recent weeks, with Sarles’s tenure ending, members of Metro’s board of directors, among others, applauded his work as the agency’s chief executive.

Yet once again, Metro is reeling in the aftermath of a fatal calamity, indicating that serious problems persist with the structural and technical condition of the nation’s second-busiest subway system.

During Sarles’s years as Metro’s top manager, the agency began an overhaul of the rail system, installing miles of new steel tracks and tens of thousands of rail ties, waterproofing tunnels, replacing vast amounts of aged electrical wiring and contracting to purchase an advanced generation of rail cars.

In a $51 million project that began several years ago, the transit authority is in the process of replacing hundreds of track circuits that allow train movements to be controlled by computers. The failure of that system, called automatic train operation, is what caused the Red Line disaster.

Much more money is due to be spent on an array of other projects. Metro is four years into the six-year, $5 billion capital improvement plan that it adopted after the 2009 crash.

While the cause of the Red Line crash was mainly the failure of automatic train operation, Monday’s incident might have involved several problems, experts said.

The NTSB, which is overseeing the investigation, has released limited details about what happened. Investigators are reviewing maintenance records for rail cars and for track, signal and power inspections; they also are looking at maintenance and repair records for the tunnel ventilation systems and reviewing the agency’s emergency response Monday.

One significant question involves the operation of fans in Metro’s tunnels, which are used to remove smoke during emergencies and to circulate air. The fans can pull or push air in different directions and can be operated remotely by Metro’s control center.

According to a preliminary NTSB report, the control center activated the tunnel fans near L’Enfant Plaza at 3:16 p.m. Monday, about a minute after the southbound train left the station and stopped in the tunnel, having encountered “an accumulation of heavy smoke.”

Video and witness accounts provided by passengers and first responders suggest that some of the fans weren’t working properly or were incorrectly activated, moving the smoke in the wrong direction, one transit expert said. He said the fans are powerful and, when used correctly, can remove smoke quickly.

Because the fans are installed in wet environments and are prone to rust and corrosion, they have to be tested and serviced regularly, the expert said.

Maintenance records for the fans have not been kept current, and some fans often are manually turned off, especially during the winter, to prevent track maintenance crews from getting cold while they work, one Metro official said.

Over the past several years, the agency has awarded millions of dollars in contracts to overhaul its tunnel ventilation systems in fan and vent shafts, which are exposed to brake dust, extreme air pressure and moisture.

Concerning the smoke and fire reports, the Tri-State Oversight Committee, which monitors the safety of Metro, raised concerns about the number of incidents last year and asked Metro whether the trouble was “indicative of a more serious problem,” committee minutes from last August show. Metro replied that it was working on solving the problem.

Federal investigators have not used the word “fire” in their statements about Monday’s incident. But within the transit agency, there were reports of four fires on the rail system around the time of the L’Enfant Plaza crisis, one on the upper level of the station, according to the longtime Metro official.

It’s not clear whether that fire was the electrical meltdown. The three other fires were on the upper and lower platforms of the Gallery Place station and near the Mount Vernon Square station.

The origin of Monday’s fatal incident was “severe electrical arcing” involving cables feeding power to the southbound third rail in the tunnel near L’Enfant Plaza. When such a system is operating properly, electricity is contained within the cables and the rail. Arcing occurs when electricity escapes and can result in sparks, heat, melting and smoke.

Although the NTSB has not said why the arcing occurred, it can happen when cables are poorly maintained and begin to deteriorate. Photos released by the NTSB show extensive damage to cables and the third rail at the site of Monday’s incident.

Metro, transit experts noted, is constantly battling water. Stations and tunnels are prone to moisture damage, leaks and, at times, flooding. The agency’s effort to fix damage caused by water and replace aging equipment is never-ending, the experts said.

Infrastructure — including cables — deteriorates more quickly in damp environments, they said. About two weeks before Monday’s incident, there was water “intrusion” in the tunnel near L’Enfant Plaza, a Metro official said. But he cautioned that it was unclear whether that was a factor in the subsequent electrical problem.

If there was damage or deterioration to the cables, it could also affect the ability of the cable insulation to do its job, one expert said.

“The insulation is synthetic and would deteriorate over time,” he said. After looking at damage photos included in the preliminary NTSB report, he said, “there was a tremendous amount of heat and electrical energy that melted the insulation.”

Throughout his five-year tenure, Sarles said again and again that he had inherited a subway system in disrepair. Previous Metro administrations had put off spending money, failing to invest in wholesale upgrades to the system, he and others said.

His predecessors made similar statements, blaming earlier general managers for Metro’s various woes.

As subway ridership increased from an average of a half-million passenger trips per weekday in 1997 to 700,000-plus in 2007, Metro was required to operate many more six- and eight-car trains. As a result, miles of track laid in the 1970s and ’80s began wearing out quickly, especially on the Red Line, the system’s oldest route.

Other components — mechanical and electronic — also deteriorated, including electrical and communications cables and rail switches, Metro officials said.

The 2009 crash was caused by faulty track circuits. At the time, the movement of Metro trains was controlled by onboard computers — the automatic train operation — and a key part of the process involved electronic communications between the computers and the track circuits.

On the Red Line, track circuits failed, causing an onboard computer to drive a train near the Fort Totten station to crash into the rear of another train at an estimated 49 mph, killing eight passengers and a train operator.

“Metro was on a collision course long before this accident,” then-NTSB chairman Deborah A.P. Hersman said in releasing a scathing report on the crash. The report cited Metro’s failings leading to the Red Line crash and called for sweeping changes.

Metro’s general manager at the time, John B. Catoe Jr., soon resigned, and Sarles, a former head of New Jersey Transit, took his place. Sarles’s annual salary when he retired Friday was $366,000.

Automatic train operation, or ATO, was suspended after the crash. Only recently — after $18 million worth of engineering analyses, equipment purchases and pick-and-shovel labor to install new track circuits — has ATO begun to return to the Red Line.

In the 1990s, before the Red Line crash, Metro “got behind on maintenance because of money, and now they’re trying to catch up,” said one transit specialist who works for a consulting firm and is familiar with Metro.

“But this is very heavy construction in a very confined space in a very confined time period,” he said, referring to the difficulty of doing major infrastructure work except during the overnight hours when the system is closed to customers.

In Metro, as in any transit agency, there is constant tension between maintenance professionals and officials who oversee subway operations.

“They have a schedule they have to keep, and on-time performance means everything,” said one transit expert, referring to operations managers. “Their career depends on it, and most transit systems have incentives if you meet your [on-time] goals.”

The expert said: “So you’ve got maintenance bumping up against that, and they’re trying to do these herculean tasks in a very short window of time.”

One longtime Metro employee said the goal of keeping trains running on time almost always prevails over the need for maintenance.

“I have never seen safety supersede operations at any time,” the person said. “On paper, it is said differently, but in reality, operations rule.”

That’s also a view shared by some D.C. firefighters who say they often encounter resistance from Metro when responding to incidents in the system.

“This seems to be [standard operating procedure] for Metro for a long time,” said Lt. Stephen Kuhn, one of the first firefighters on the scene Monday. “I’m sure they don’t have it written down as ‘Go handle the situation yourself and if it’s really bad, call 911.’ But in my experience, that’s what it is.

“The push-back comes from Metro, the ones running their operations control center. They just do not want to stop trains for any reason,” said Kuhn, who stressed that he was speaking for himself and not the department.

Metro has limited options when it comes to scheduling track maintenance. The subway system is open from 5 a.m. to midnight Monday to Thursday. On Fridays, it stays open past midnight, until 3 a.m. Saturdays, then runs from 7 a.m. Saturday to 3 a.m. Sunday. That means that on a typical weekday, crews have “a narrow window” of 2 1/2 to three hours to perform labor-intensive chores, the expert said.

On Tuesday, a day after the Yellow Line train filled with smoke, Bowser (D), a former Metro board member, called the incident “shocking” and “disappointing” in light of how “dramatically” the transit system has improved in recent years.

But she soon backed away from her assessment that Metro had gotten vastly better.

“I think that there are a lot of questions that remain,” she said later in the week.

Then, on Saturday, came confirmation of the radio-communication problem.

Rep. Gerald E. Connolly (D-Va.), said in a statement Saturday that he was “very frustrated” to learn about the radio trouble, comparing them with the emergency communications problems that occurred immediately after the Sept. 11, 2001, terrorist attacks.

“We in this region have received a fair amount of money to fix this, so it passeth all understanding that we apparently are continually plagued by this communications demon,” he said. “It impedes efforts, obviously, to respond in an effective manner.”

Aaron C. Davis and Mary Pat Flaherty contributed to this report.