I too think there is a problem, whenever i equip 2 weapons, the damage decreases lower than if i had equipped one of the weapons alone.
ok i'm only lvl 1 in dual wielding but i don't think it should do that... at least in the original it didn't.
They may have made the base penalty greater. Take a look at the Duel Wielding skill and it should say how the damage of each weapon is being modified.