Vigilante Fighter Perk is not applying it's bonuses.
Have you tried resting/reapplying it through the custom tools? What exactly doesn't seem to be working?
This still happens. Most perks automatically apply most of the time, but for some reason, this one more often than not requires manual activation in the crafting menu.
I also have never received the level 1 benefit (1 potion of Protection from Chaos per reset.)