Did you use the "Unit - Damage Target" function? If you did, this function just deals a specific amount of damage to the target and it counts as if it was the source who actually attacked the target. This has nothing to do with the units normal damage. On heroes the damage is able to calculate by checking the damage dices in the object editor and then look at the Gamplay constants how much the damage increases for each point on the primary attribute. This is the way I know but unless there is only one hero you must set the dices the same for all hero types. If I remember (not sitting home with my computer right now) all heroes have the same dice vaules by standard.
Take a look att a hero Paladin for example. You see this: (the "//= x" is just comments. It's not shown.) Combat - Attack 1 - Damage Base 0 //= b Combat - Attack 1 - Damage Number of Dice 2 //= n Combat - Attack 1 - Damage Sides per Die 6 //= s
Go to Gameplay Constants and find this: Hero Attributes - Attack Bonus per Primary Att. Point 1.00 //= c
Amount of primary attribute = x
These things combined with the primary attribute decides the heroes damage.
Here are the formulas: Minimum damage = b+n+x*c Maximum damage = b+n*s+x*c
There is actually a far easier way to do this, simply go in to game play constenents edit the various armor and weapon types to your liking, then go to game play interface change the armor and weapon and armor icons and finally change the armor and weapon tooltips. Its that simple you now have your own weaknesses and strangths system.