I gotta wonder if this is related to the way that some things seem to happen with the Options menu. It's been reported that if ya change stuff there, say the game speed, that it does not really take effect till you then hit "Play" on that village/tribe. Wonder if that is the case with pausing from the Options menu too?
One thing to try it to pause the game using the spacebar ... THEN quit.
Jer
We make a living by what we get, we make a life by what we give.