In PCGen, the Giant creature template gives a +3 to natural armor, regardless of original creature size (reference- http://paizo.com/pathfinderRPG/prd/monsters/monsterAdvancement.html#_giant-creature). However, in PCGen I'm getting the wrong bonus to natural armor for creatures of certain original sizes:
Small, Diminutive, Fine: +1
Yeah, it's following the size rules. I can override that, but then any enlarged people will be
annoyed. On my todo list - Giant Sized overrides Size Rules. Check.
Fixed as part of other work.