[scigeek42]

In the book it describes how the difficulty with the calculation came from the fact that they were continuously firing the spacecraft thrusters (it was some form of drive that used a constant small acceleration). Thus far most all of our probes use short-term bursts to change their velocities. I'm not sure how many ion-engine equipped probes we have that have needed to calculate multiple slingshot manoeuvres.

In his interview with Adam Savage the author described how he wound up writing his own custom code to calculate the trajectories of their spacecraft. One could imagine that NASA would need to consider a lot more "real-world" variables than a sci-fi author, so it is somewhat reasonable to think time on a supercomputer could have come in handy.