Easiest answer: heterozygote advantage.

meant to say: "if you have exactly one copy of the gene, it's better than zero or two copies." Can you edit post-submission?

The message of the paper and the literature as they read it is: if you have exactly one copy of the gene, it's better than zero copies. It's like malaria resistance and cycle cell anemia. See "heterozygote advantage" on Wikipedia. From the paper: "We show that a lifespan-extending variant of the human KLOTHO gene, KL-VS, is associated with enhanced cognition in heterozygous carriers.... Three percent were homozygous for KL-VS, a rare genotype that for unknown reasons is associated with decreased lifespan and detrimental effects (Arking et al., 2002, 2005; Deary et al., 2005); they were excluded from the study." If you have two copies, it's worse than zero. So if nearly everybody had two copies of the KL-VS variant, then children of the rare people with 0 or 1 copies would have a fitness advantage relative to the population. A dynamic like this would prevent it from going to fixation. (Assuming it just has an additive effect with other genes etc.)