Long story short:
Civ4 is notorious for passing garbage into functions. It loves trying to see if player 204958 has any cities, even though the max player # is 50. This often causes CTD's if the function isn't protected against executing garbage. Usually, simple in-range checks suffice, making sure that the player values are all within the normal bounds. I proceeded to do this with some of the Fixed Borders functions. Unfortunately, I failed to realize that one particular function was meant to receive invalid data (expanding fixed borders over unclaimed territory. The unclaimed territory is owned b player -1, or NO_PLAYER) and process it, but I had added a check to stop invalid data. The game couldn't expand the territory, and so an infinite loop ensued.
Hat's off to Dexy for correcting it.
@Os79, I am unsure how much space making an fpk will save, but I'd be interested to see the results none-the-less.