Unless the target has cold resistance, it will deal 100% damage. Defense does not mitigate magical damage in any way.

Well yes, but they seem to do a lot more damage to units with lower level armour than higher. Say you have a bunch of guys in leather and a bunch in plate. The plate will take a lot less damage from an ice staff than the guys in leather, yet they both have 0 ice resist. I've seen this repeated. I'd like to know how other things that factor in to protect a unit from the amount of magic/ice/fire/etc. damage as opposed to a sword or spear.

Is it broken? I have noticed my ice mages dealing less damage against enemies with cold resistance or more against enemies with things like Quendar blood (-50% cold resist), but they seemed to be dealing consistent damage to everything else. I'm pretty sure it's working as intended, though maybe check the enemies' traits and equipment a bit more closely. It's also possible it's just bugged for plate mail.