Why does it take longer if you microwave something twice than if you microwave it once?

I had a problem when I microwaved a mug of soup that it would tend to splatter the microwave. I tried cooking for a shorter time, taking the soup out of the microwave, mixing it to even out the heat distribution, and cooking it again. That eliminated the splattering, but the total time for cooking is longer. Why should that be? Is there some overhead at the start?