Were both characters exactly the same? I was just thinking after reading your post that if you create a ... say mage character, he would have no armor so his resists would be lower than say... a warrior, who would have some armor on at creation. Just a thought as I'm not able to test this out at this moment.
Then you'll need to remove the armor from character templates that have it. Go to CharacterCreation.cs around line 540 and down you'll find the equip items statements, you'll need to change any of those that have resist to some thing that doesn't. Like change them all to the same items the mage starts with, which is just clothes items with no resist. If you just comment or delete those items, the characters will all start naked.