I have uploaded a new version of this plugin that should correct this issue.
This plugin wasn't using the same exact function as the optimize command on the equip scene, due to them being in different scenes, and my general lack of experience at the time. I'd managed to get it to optimize equipments using the actor function, which was a small part of the optimize command, but it ignored anything added to that command by other plugins.
Now I have gone in and made this plugin use the exact same function that the equip scene uses when you use the optimize command there. That should make changes made to the optimize command by other plugins carry through to this one, and should make the two different functions identical. Hopefully fixing your optimize issue.
As for your shield thing, dual wielding two weapons and also a shield is not something that is technically supported by this plugin. A dual wield actor has two weapon slots <1,1, armor slots> and I have modified the second weapon slot to also allow type 2, so it's effectively <1, 1/2, armor slots>. If you use equip core to give your characters an extra shield slot, a normal actor would have <1, 2, 2, armor slots> and a dual wield one would have <1, 1/2, 2 armor slots>, causing both types to be able to wield two shields.
However, and I haven't tried this myself, so I can't guarantee it won't cause other problems, lines 1453-1455 are the check that includes shields in the offhand weapon slot as equippable items. So you could comment out those lines and dual wield actors would no longer be able to wield a shield in their offhand slot. This would allow you to put in a shield slot for dual wield actors without allowing them to have two shields. You'd have to find a way to only apply it to the dual wielding actors though, as if non dual wield actors also have this extra shield slot, they will still be able to wield two shields.
Also, if you're using my shield block plugin, you're gonna run into some problems with it actually detecting the shield for blocking, as it checks the offhand slot exclusively for the shield.