How can a 1,000-year rainfall not result in a 1,000-year flood?

It comes down to a number of factors, including the pattern of movement of the rainstorm in each particular watershed, the conditions of the soil and plant matter in the watershed, and the timing of the rainstorm in one watershed versus other watersheds.  

For example, if the ground is already saturated before a rainstorm, much of the rain will run off into streams, but if the ground is dry, it will soak up more of the rain and the runoff will be less significant.