It's a known engine bug in NWN1 that some of the properties of the main hand weapon are erroneously imposed on the off-hand weapon. I can't remember for sure if energy damage type is one of the things that gets transposed, but that would explain what you're seeing.

OK, that explains some things but this is happening in NWN2 and is driving me crazy since I made 2 swords with 2 different typed of elemental damage to cut trough any elemental resistances and/or immunities and now only my main hand elemental damages are affecting the enemies... I've been thinking of adding some special effects like "silence", "sleep) or "blind" but I don't want to waste the essences if those don't work either... Any advise from people who have experience in this?

Out of curiosity, I hopped into NWN2, and the magic damage of my character's off-hand weapon was occurring fairly regularly.
Have you literally been seeing only 100% main-hand damage effect, or does the off-hand damage effect show up sometimes? If that's the case, it might just be that you're not hitting very often with your off-hand, maybe from attack penalty, or the fact that you can only swing an off-hand once per round, (without extra feats). I'm just throwing guesses out.
A glitch wouldn't surprise me, either, as I've seen NWN2 do silly things before.

Do you have the dual-wielding feats? If you don't, you're only getting one off-hand attack per round -and that at a substantial penalty.

I have epic two-weapon fighting, and yes for some reason I only see 100% of the main hand elemental/magical damage. This is driving me nuts since i have used considerable time to craft my dream weapons. I even tried reinstalling the game to see if this was caused by corrupted files or something, kept happening. Out of frustration for the diminished damage I downloaded Charlies Item Property Changer and added the lost damage as an ordinary damage enchantment... Works like a bandage for getting the desired damage but not the elemental damages...

Are you absolutely certain the damage is not being applied to your opponent(s)? I know the NWN engine is spotty at best in reporting what's actually occurring, so this may be a case of the damage actually firing, but the engine not reporting it in the battle log.

That's actually a really good point... Do any of you guys have an idea on how to test this? Maybe I could make an healing sword for an off-hand weapon (with charlies item modifier) and see if the monsters get healed or something... Or make an negative energy weapon for an offhand (and a weaker positive energy) and attack some zombies and see if they're healed since this is an problem with elemental damage.

Create a test character with minimum strength. Create two enchanted daggers, one with very high fire damage bonus and one with very high cold damage bonus, and equip the cold damage weapon in your off-hand. Then go and fight a fire elemental. Your physical damage should be reduced to about 1-3 damage per hit, so cold damage against a cold vulnerable creature should be extremely noticeable.