A recent data change to Ioun Stones has resulted in the fact that the enhancement bonuses to ability scores are displayed differently from enhancement bonuses granted by other equipment:
For example, for a character with a Dexterity score of, equipping a belt of incedible dexterity +2 will result in a Dex base score of 10, and a temp score of 12 on the output sheet. Equipping a deep red sphere ioun stone, however, which also grants a +2 enhancement bonus to Dexterity displays both values as 12.
This is caused by the change to move the bonus from the equipment object into an ability object that is granted when the item is equipped. Thus, PCGen can no longer identify the bonus as an equipment-based bonus.