Cbea20,
I can't answer your question except to give you the link to TransNica's schedule.
http://www.transnica.com/tariffs_schedules.htm
Either Tica Bus is sandbagging their schedule or TransNica is overly optimistic. From what I remember the immigration office was virtually empty at the time we arrived (between 4:30 and 5:00 p.m.) and there were less people to process due to the fewer number of seats. But I have no idea why it would take Tica Bus 1 to 2 hours longer with almost the same departure time from San Jose. Perhaps there are no intermediate stops between SJ and Managua. I'm just guessing but its something that should be checked out.