To get back to the question (if that's OK
)... could there be a Wisdom modifier involved? Meaning that Wisdom (or possibly Intelligence) is too low to be triggering the "I smell your evil aura" (or some such) response?
I also use the "remove class restrictions" mod for my Pally (who is also Chaotic Good)-- and iirc I didn't have that problem when she talked to the nasty child-stealing witch. It's been a while since I did it, but as I recall, one time I talked to her with my negotiator in order to check her wares. When she didn't have anything worth buying, I had the Pally talk to her, and suddenly the kid popped up and started screaming, and we were in a fight --which we nearly lost due to Witchzilla's area-effect spells (or those of her summonses). I was too busy trying to keep everybody alive to even tell who was casting those blasted Chaos spells. I can definitely say that we did not have to go asking around town about her to figure out who was stealing the children.
So I don't think it's the mod.