Also, to add, issue fixes completely when using the setting for "Start/Stop at N Height" and just setting the start/stop point for each of my processes at the color switch point.

Problem is: what happens when I do dual extrusion prints that are multiple colors on same layer or even switches every layer? BIg problems.

I'm surprised at the lack of support over at S3D's site. I've made two topics on there in the last day or so with no response. I had always heard their support was great.