I see what’s going on now. It’s not that the class isn’t giving me my magic bonus, it’s that my hero isn’t getting magic bonuses from any of the kingdoms that give magic bonuses for maxing out the kingdom level.
In the past I’ve had a total of 18 damage from War & Peace:
9 from the weapon
5 from being a Mechanist
4 from 4 Kingdom bonuses
Now I’m not getting any bonuses from the kingdoms, so my weapon’s damage is down to 14. Right now I can’t tell if the other kingdom bonuses are being applied to my hero or not. I think they are, but I can’t seem to find any list of what the base stats of the hero are supposed to be.
I have also switched to a different class and back to Mechanist and the issue is still present.