I have tagged slaver perk and it does show appraise +3 bonus but does not show intimidate one. Not sure if it should even be considered an issue as it's pure RP skill.
Is this after resting/relogging/transitioning and all that stuff?
If you get the appraise, you definitely get the intimidate. Check again.
My bad, I forgot the skill checks from ability modifiers, exact 3 point difference mislead me.