I made a new project and just using your plugins and the other plugins needed, such as auto-passive states (for the shields to have shield blocking enabled). It also is not working right with just the YEP Core Engine, Battle Core, & your Duel Wield plugin.
I am still getting two dual wielding attacks when I used the dual wielding attack skills, whether a double strike or attack on all enemies. It works fine for regular attacks, but skills with action sequences are not working for me. I am still getting double attacks when using a two handed weapon or shield. (The problem exists for the modified plugin and the original, v2.69.)
An example of a dual wielding attack skill notebox:
<Dualwield Skill>
<Whole Action>
dualwield action: 6
motion attack: user
motion wait: user
action animation: opponents
wait for animation
action effect: opponents
death break
</Whole Action>
<target action>
</target action>
Edit: I think I found a simple solution! I noticed that the plugin has a state for disabling dual wielding. I added that to shields and two handed weapons, and that seems to be working!