It could be because of an unpublished "dwell time" somewhere along the line.

I've had the same experience. For some reason, when I try to book a multi-city trip thru NLC, it always chooses the next later train. It doesn't matter if I try KIN-OSB (via NLC) or BOS-OSB (via NLC) - it's always the next train at NLC! And it doesn't matter which direction - N or S.

(I have no choice but to use NLC as a stop. The only way to get a 4 segment trip from KIN to OSB is to include NLC as a stop.)

BTW - there is no dwell time (as far as I know) at NLC! I've been at the station (off the train) many times and have seen the trains leave as soon as they get there!