-EDIT-
It was the window padding parameter in Yanflys Core Engine. If I have it set below 16, it shows the duplicate craft command.
Okay, one more update for the night. I took 2 screenshots, 1 of the 5 slot system edit and one of the normal setup.
Above is the 5 slot system.
Above is the 4 slot system. I do notice that the category and level text is closer to the separating gauge than in the 5 slot image, but I'm not sure why. I have disabled quite a few plugins, especially any that I immediately thought could be conflicting, but no luck yet.
Oof, sorry to keep nagging like this but I have made some progress. After copying my project and disabling the plugins by category to pin it down, it wasn't until I finally disabled Yanfly's Core engine and Updates core that it was finally resolved. But that left me more confused, as I don't understand why that could be, unless its because I modified the Core plugin in this project. When I copied the plugins.js file from the new test project that was working properly WITH the core installed, it worked. So somewhere in my plugin data I have something causing this issue.