The game may have messed up the resistances upon removing your dragon armour with the Magic Barrier bonus (though if that happens it is more often when the skill was not otherwise known), which could grow progressively worse whenever you remove your equipment (visiting the dwarven king, etc) or otherwise do something to get the game to update your resistances. There could also potentially be a problem if the sum of the levels that you learned yourself and the equipment bonus (usually) add up to 5 or more (at least one person said they only had an issue if the total was over 5, another said it happened to them at 5, as well). Since you started with level 3, either the problem is triggered even at a total of level 4, or you have more than one Magic Barrier equipment bonus... or the sum of the skill levels wasn't what trigger the problem.
There are a couple ways you can fix your resistances. The values can be edited directly (see the topic
Some more hex offsets..., and possibly
Teleporting Anywhere, via hex editor as a reference).
Alternately, if you learn Magic Barrier (if you have the level and skill points to do so), save, use
iZakaroN's SaveEditor to unlearn the skill, reload the save, learn the skill and save again, and repeat using the save editor to unlearn the skill, you can keep doing that to restore up to 25 resistance each time.
To keep this from happening again you can use DAD's Item Editor (link below) to re-create your dragon armour by editing another breastplate in your inventory to have the same stats (you can add resistance bonuses rather than the skill bonus, and give yourself a skill point to learn Wisdom). You only need to wear the complete dragon armour set once to finish that quest, and have Bless cast on you (temporary effect); there are no set bonuses.
Alternately, make sure you end up with at least 1 but less than 3(?) levels in the passive Magic Barrier skill. Or since it triggered when you already knew the skill, you could try unlearning it completely.
There is a similar issue with the sight range skills (
please help with my blind hero).
EDIT: Here is a mirror link for version 1.4 of
DAD's Item Editor.
If you do not already have the Visual Basic 6 redistributable installed, and get missing file/component errors, use the
full installer for v1.1, then replace the executable in the install folder with the latest version.