ABC News reports:
Metro-North, the nation's second-busiest commuter railroad, was brought to a standstill for nearly two hours on Thursday night after computer problems caused signal issues system-wide, railroad officials said.
CBS has this diagnosis of what went wrong, and why
The cause of the outage remained under investigation Thursday night. “We can’t say what the cause of it is. We’re still trying to figure that out,” Daniels told 1010 WINS.
For a good read on after-incident reporting, I always refer people to the Postmortems group on Google+ - it's an excellent source of descriptions of what happened when computers "glitch" (because they rarely glitch all by themselves).
UPDATE: AP/WSJ The Metro-North computer "glitch" described as human error, AP story:
MTA head Thomas Prendergast said Friday that computers that run Metro-North's signal system lost power at 7:45 p.m. Thursday when one of two main power supply units was taken out of service for replacement.
He said technicians performing the work did not realize that a wire was disconnected on the other main power supply unit.