PCGen is applying the attack benefit to all attacks with 2W-OH and to 1H-O.
"Made from a mix of sturdy steel and boiled leather, these vambraces grant a +1 deflection bonus to AC while the wearer is wielding a double weapon or two weapons (not including natural weapons or unarmed attacks). "In addition, once per round, when attacking with an off-handed weapon, the wearer can reduce any penalties on attack rolls made with that weapon by 2."
The apparent disparety with the term "once per turn" (singular) and "attack rolls" (plural) is reconciled by the fact that one attack by an off-hand weapon can include multiple attack rolls (such as attack rolls to confirm critical hits). So the benefit should only apply once per turn, meaning to ONE off-handed attack (and any additional attack rolls which are part of that one attack). It could also apply to a single attack by an off-hand weapon (for example if the PC has a cold iron weapon in the primary hand and an adamantine weapon in their off-hand) but has only a single attack action. This reduces ANY penalties associated with using that off hand weapon, not just ones related to TWF or using a double weapon. And it doesn't always have to be the first attack either.
There are two situations here, when the off-hand weapon gets only a single attack, then it is logical to always apply the bonus. However, on a crit build character with multiple attacks a player might not want the bonus on the first attack. Since the wording allows the bonus to be applied once per turn and doesn't specifically state that it has to be the first attack, I don't think PCGen should apply the bonus to the weapon block at all when there are more than one off-hand attacks per round. It should be left up to the player to manually apply the benfit to whichever off-hand attack they want. For consistency of implementation I dont think the benefit should be applied to the weapon table even if there is only a single off-hand attack and no other choice, because it will cause confusion as soon as the character gains the ability to have multiple attacks with an off-hand weapon.