The issues caused some train cancellations and delays Sunday morning.
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NJ Transit and SEPTA were also affected.
Four Regional Rail lines were impacted, including the Airport, Trenton, Newark and Chestnut Hill West lines.
"It was initially an hour delay, from there it was two hours, three hours and then they canceled it around like 9," said Emerald Pierce of Charlottesville, Virginia.
After a week of holiday fun, Emerald Pierce says she was trying to get to work in Virginia.
She arrived at the train station at 5 a.m.
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Six hours later, she was still there.
"I'm tired, the kids are frustrated. They're not really giving us any information right now, it's just a waiting game," said Pierce.
Amtrak workers directed passengers to have patience as they worked to figure out what was wrong with the train system.
With New Year's Eve plans on the line, riders were left to figure out what to do.
"I'm about to start walking, I'm making it to Atlantic City for New Year's, baby!" said Sara Sanchez of Lancaster, Pennsylvania.
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Other people opted to drive to their destinations, like Dan Hoelzle who purchased tickets for him and his son to see the Ravens-Dolphins game in Baltimore.
"We're not going to miss the game, that's all I can tell you," said Hoelzle. "It's very frustrating."
The signal was resolved around 11 a.m.
Amtrak says there will continue to be residual delays.