I think it's something like this: skills are divided into tiers, which you can learn at different character levels: 1, 4, 7, 10, 13, 16, 18, 20.
With ability Rank 1, there is no additional AP cost for level 1 and 4 skills, but each level past that gets a +2 AP cost penalty per tier.
With ability Rank 2, there is no additional AP cost for level 1, 4, and 7 skills, but level 10+ gets a +2 AP cost penalty per tier, and so on.
There's sort of a grace period built into it, but if you want to use skills which require level 7 with no AP penalty, then you'll have to sink a second point into the associated ability.