Alright, we got there.
So there were a couple of things going on here, and I suspect the issue you're having came up after the v2.68 update, as a result of what I found and fixed just now.
That update reverted a change I'd made the the battler.isDualWield() function, namely, that prior to v2.68 it returned false in battle, if the actor that was being checked was not actively wielding two weapons. When I reverted this function, I made a different function battler.isCurrentlyDualWielding(), which was meant to essentially do the same thing as the function above did. The problem is, when I made that, I missed a couple of places in the plugin where I'd used the isDualWield function, namely the action sequence code, which is why the skills with the dualwield action: x command in them weren't working right.
Basically the plugin thought the actor was actively dual wielding, so the skills which used a check to see if the actor was dual wielding would continue as if he was. There were also other issues with it. Skills that hit multiple times would only actually swing the weapon one time, as the action sequence would try to pull the motion attack type from a weapon that didn't have a wtype (the shield), causing the actor to do nothing instead. And every skill used by a dual wield type actor who had a shield in their off hand would also always deal damage as if it were the offhand weapon being used, which, because they had a shield, would be a lot lower than it should be.
I have corrected the problems you've been experiencing in the latest version 2.73, which should be uploaded in a couple of minutes. It also includes an attack times+ fix that should mean you won't need to modify the plugin anymore either.
I apologize this took so long to track down.
~Ramza