When summoner achieves level 1, 6, 12 (and every 6th level), the Ability Increase evolution for the Eidolon is legal to choose. (this is specifically referring to the evolution, not the ability score increase at 5th class level for the Eidolon).
PCGEN is not allowing Ability Increase evolution to be purchased more than once.
"The following evolutions cost 2 points from the eidolon's evolution pool.:
Ability Increase (Ex): The eidolon grows larger muscles, gains faster reflexes, achieves greater intelligence, or acquires another increase to one of its abilities. Increase one of the eidolon's ability scores by 2. This evolution can be selected more than once. It can be applied only once to an individual ability score, plus one additional time for every 6 levels the summoner possesses."