From the article linked to above, it may be an issue of the system being disconnected, so the AMTRAK never got the signal.
Again, just from the new article..
"The CSX train was sitting on a side line known as the industry line, according to a source familiar with the matter. A switch that was supposed to send the Amtrak train down the cleared main line was not in the proper position and sent it down the industry line instead, the source said.
Typically, an automatic signal would have warned that the switch was in the wrong position, instructing the engineer to slow down. However, a crew had recently been working on the system in that area, and it may have been shut off when the incident occurred, the source said."
