Unfortunately, weapon unleash isn't exactly compatible with the dual wield plugin, so I wonder if the problem is coming from that?
Can you try, for experimentation sake, using the twohanded weapon without weapon unleash to see the 'normal attack' skill that it would usually use and see if it also hits twice? I'm not entirely sure how weapon unleash codes its skill usage, but dual wield only 'detects' a skill as dual wielding automatically if it's the first skill in the skill list, or if it's tagged specifically as a <dual wield> skill, but the only effect this would have would be to have sequential attacks switch weapons (and damage) within that skill.
Moreover, the problem seems to be that the game is deciding that your actor is dual wielding, when he's not, which is triggering the extra attack even when he isn't.
During battle, can you open the console (f12) and put in the following script?
$gameParty.members()[0].isCurrentlyDualWielding()
Replace the 0 with the index of the party slot where the guy with the two handed weapon is. If he's the lead, he'll be index 0, if he's the second in line it's index 1, etc.
For someone who's actually actively got two weapons equipped, this should return true, but for someone using a twohander, it should be false. It should also return false if you have the barehanded attack parameter disabled, and he's got a one handed weapon and nothing in his off hand, or if he's got a shield in his offhand.
If that's coming back true, we probably know where the problem is, it's that the engine is detecting the user as dual wielding when he's not, and I can go from there to figure out why.
If it isn't detecting him as dual wielding via that script, then something is adding an extra attack to your skill, and that could be the skill unleash incompatibility I was talking about earlier. The dual wield plugin does make some 'secret' changes to the action sequence of the attack skill, and to any skills tagged with the skill tags.
It could also be something simple, like a trait adding an extra attack to the actor, which would also make the regular attack skill hit twice.
~Ramza

Something else i would also like to clarify is that the dual wield weapons are using the same notetag, so its not interchanging notetags with one another, in fact, i had to acutally alter this a while ago and remove a couple of weapons because i couldn't get them to behave like RPG Maker 2003's Weapons nor could I locate a proper solution)