Just a day after full service was restored at Penn Station following Amtrak’s summerlong repairs there, a problem inside one of the tunnels connecting to the station delayed about a third of LIRR Wednesday morning rush-hour trains.

A stalled Amtrak train inside one of the East River tunnels resulted in 44 of the LIRR’s 144 morning rush-hour trains running late, the railroad said. Most of the delays were in the range of 10 to 15 minutes, but one train was 41 minutes late. In addition, the Long Island Rail Road canceled one train and diverted another from Penn Station to Atlantic Terminal in Brooklyn.

The disruptions came a day after Penn was returned to full strength following Amtrak’s eight-week infrastructure renewal project at the Manhattan station. The work required taking several tracks out of service at Penn Station, which serves some 650,000 customers each day.

Despite the reduced capacity, the LIRR performed better in July and August than it did in months. Problems at Penn Station and in the adjoining tunnels that snarled many a rush hour in the first half of 2017 were few and far between during the summer months. Amtrak, which owns and maintains both Penn Station and the East River tunnels, said it pre-positioned extra crews and equipment during the summer to respond more quickly as incidents arose.

In a statement, Amtrak spokeswoman Christina Leeds said the stalled train Wednesday morning was caused by “an equipment issue, not an infrastructure issue.” She said Amtrak’s regularly staffed “protect” crews and equipment responded to the incident, which “took about 30 minutes to clear.”

Amtrak reported the issue to the LIRR at 8:27 a.m. and said it was cleared as of 8:34 a.m., LIRR spokesman Aaron Donovan said.

On social media, some commuters expressed concern that the incident signified a return to business as usual at Penn Station, following the heightened attention paid to it by Amtrak and the LIRR during the summer. MTA chairman Joe Lhota has promised that its improved management and communication with customers is here to stay, but has also noted that the condition and upkeep of Penn and the tunnels are out of the agency’s control.

West Hempstead LIRR commuter Jake Adler said his train “sat outside Penn” for about 15 minutes because of the stalled Amtrak train.

“It wasn’t the worst delay I’ve been in, but it definitely wasn’t something that anyone wanted in September now that we got through the summer,” Adler, 31, said. “It’s disappointing because even when the LIRR gets it right, we are at the mercy of Amtrak.”

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