After turning off a bunch of scripts I found it was the Yanfly Battle Core Engine that seems to be messing with it when I turn it off it works. Does anyone know why this is? I was looking through the scripts and can't figure it out. Thanks in advance.
I know this doesn't help your problem, but I've found Yanflys battle plugin causes issues with just about every battle plugin I've ever tried. I highly recommend not using it if you plan on having any non-YEP Battle Plugins.
I've taken a look at the plugin and I see something about action sequences in the HELP portion on the bottom. Maybe it has something to do with that?