I remember reading when this close call happened, that both the CSX and Amtrak train were placed into emergency braking. It sounds to me that the alerter was ignored because the engineer was asleep and the train was automatically put into emergency braking. Then again doesn't the alerter go off every 60 seconds? which would make me beleave that the engineer somehow hit the alerter button while he was asleep, kind of like what you may do in the morning hitting the off button on your alarm clock without waking up and going back to sleep.
Something else I thought off too is this... ( I guess this would depend on how far apart the blocks are set on this stretch of track) As the CSX train was aproaching signals toward the Amtrak train, the CSX signals should have been getting more restrictive as he was getting closer to Amtrak, to the point of even having a STOP or RESTRICTING signal. The CSX engineer may have had a CLEAR or SLOW CLEAR a block or two back then all of the sudden run upon a RESTRICTING or STOP signal. IF this happened it may have tipped off the CSX crew that something wasn't right.
I guess I don't understand how the Amtrak train ran at least a couple STOP signals (acording to one report I read) and the alerter didn't put the train into emergency earlier then it did without the engineer hitting the button somehow in his sleep.