Hey there, I'm happy the first fix should be easy at least=). So yeah I have the dual wield slot type like above added to all dual wield classes and their equip slots is set like this.
<Equip Slot: 1, 1, 3>
As for turning off the plugin, you're right it does still remove the slot 3 item only when there is a 2 hander in slot 1. So the exact same thing happens with the plugin off. Does that mean it's yanflys equipment restriction plugin?