Standing at Rahway station around 6:30pm I see some not in service Jersey Arrow IIIs speeding by at 125 mph as they were originally built thus now restricted to 80mph with passengers on board and due to age. I also notice that some NJT trains use the first two northbound tracks as they’re heading south from NYC. Why are those south bounds using the first two tracks? Some freight trains also use the first two northbound tracks when they head south. http://en.wikipedia.org/wiki/File:Rahway-njt.jpg
The NEC 4-track main from Trenton to Newark is signalled for bidirectional operation on all four tracks. The dispatcher will select tracks according to operating efficiency without even considering the history of which tracks were northbound and which southbound, except for platforming local trains. And he will probably not use the same mix at the same time every day. If a freight was part of the mix, it may have been the decisive factor. Which side of the RofW are sidings its needs to switch (picup up or drop a car or cars)? Also which tracks may be out of service for maintenance can effect his decisions. Similarly, repairs or overhauls to local station platforms. Note that your sighting was during the end of the evening rush hour, predominantly southbound.