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(The following article by Vincent M. Mallozzi was posted on the New York Times website on July 21.)

NEW YORK — New Jersey Transit and Amtrak got their signals crossed — and a few of them crushed — last month during a test run of one of the two-tiered trains that will debut this fall.

On June 8, the first of New Jersey Transit’s planned fleet of 231 bilevel trains, which cost about $1.9 million each, slipped out on a midnight test run to New York.

Built taller and wider than traditional suburban commuter trains, the ‘double-decker’ had difficulty passing through one of the two tunnels heading into Pennsylvania Station, tearing down two signals as it chugged past the west end of track 5.

Cliff Black, a spokesman for Amtrak, confirmed that the train had done some damage during its test run, and blamed the accident on low-lying signals hanging in the station. He said that no passengers were on board that night, and that the train’s engineer and its conductors were not injured.

“As a result of this incident, a test was made within the station to review any signals that might not comply with the new bilevel equipment,’’ Mr. Black said. “Any noncompliant signals will be adjusted.’’

Hélène Gagnon, a senior director of communications for Bombardier, the Canadian company that made the bilevel trains, said adjustments were being made to ensure that track signals are placed high and wide enough to accommodate the expanded measurements of the new trains.

“We run the cars on low speed to verify whether they clear all elements on the routes where they will eventually run, such as tunnels, tracks and signals,’’ Ms. Gagnon said. “It was determined by Amtrak that its signals department had installed signal lights that did not conform to the Amtrak clearance profile.’’

By that, Ms. Gagnon meant that Bombardier was not responsible for last month’s incident.

“The bottom line is that Bombardier’s new railcars were within the clearance envelope allowed by Amtrak,’’ she said. “And if the signals were properly located, the car should have cleared all signals.’’

Ms. Gagnon said she was told by Amtrak that an estimated 25 signals had recently been installed by a new vendor, and that the new signals hung lower from the ceilings of the two tunnels than the ones they had replaced.

“We are confident that Amtrak will take appropriate actions to ensure clearance of the new cars,’’ she said.

Mr. Black said that Amtrak “did not know for sure if the signals were installed incorrectly, but they certainly did not conform to the profile.’’

As for the railcars themselves, Mr. Black said: “As far as we know, they are compliant.’’
A spokesman for New Jersey Transit, Dan Stessel, said that the train that tore down the signals suffered only “minor cosmetic damages.’’