It came down to who got to ship first in the last time (wife had a lower faction number, so she got it).

I'm not sure how it can come down to who gets to ship first, but it's been a while since I played this game. I wonder if you have a rule wrong, so I'll clarify it here just in case:

The pile of VP chips (12 per player) is the countdown to the end of the game (well, 1 way to end the game). But it is not all of the VP chips available to get. Once the pile runs out, get the other VP chips out and use them to finish that round.

On the other ending too - when someone builds their 12th development/world, that round finishes before the game ends.