Updated Feb. 5, 2015 9:33 p.m. ET
The flashing lights and crossing arms worked, and so did the traffic signal.

The engineer of the Metro-North train sounded his horn and applied the emergency brakes before the train crashed into the vehicle Tuesday night.

Thursday evening’s briefing by the National Transportation Safety Board showed that warning systems appeared to have worked properly, but a central mystery remained: Why the driver of the sport-utility vehicle, Ellen Schaeffer Brody, didn’t quickly move after stopping on the tracks in the Westchester County town of Valhalla, N.Y.

Ms. Brody and five passengers on the train died after the northbound commuter train struck Ms. Brody’s SUV, pushing it down the tracks and leading to a fire that engulfed the front of the train.

Federal investigators are still working to identify the causes of the accident, said Robert Sumwalt, a board member of the NTSB, at the Thursday night briefing.

The flashing red lights at the intersection of Commerce Street in Valhalla illuminated 39 seconds before the crash. A few seconds later, the crossing gates came down, as they were supposed to, Mr. Sumwalt said.

Another so-called pre-emption device that triggers a nearby traffic signal before trains approach—aimed at preventing a traffic jam—was also working, Mr. Sumwalt said.

“They both operated as designed,” Mr. Sumwalt said. “There were no problems found with either.”

The electrified third rail, which powers the railroad in this section of the system, sliced into the Mercedes SUV and the commuter train, according to officials investigating the crash.

NTSB investigators spoke with a driver who was directly behind the SUV at the crossing. That driver told investigators that traffic was “inching along” as the SUV slowly moved into the crossing.

When the SUV stopped, the gate closed on top of it, resting on the back window of the vehicle, investigators said.

The driver said he motioned with his hands and attempted to communicate with the SUV’s driver to back up. The SUV’s driver got out of the vehicle and touched the gate before getting back inside, he said.

Mr. Sumwalt said the safety board would release more detail from the interview with the train engineer on Friday.

The engineer, Steven Smalls, was released from an area hospital on Wednesday, said an attorney for a union representing Metro-North employees.

The Metro-North Railroad resumed service on its Harlem line Thursday morning.

—Mark Morales contributed to this article.

Write to Andrew Tangel at [email protected]