I was going to see if I could send some parts of the project, and I thought of maybe first I should remove all the templates and readd them. That seems to have fixed this so who knows what was wrong.
However, there are 2 more things that are a bit odd with this that I must ask about.
First, when I removed and readded the templates, Playmaker added a component called "fixed update", but only on some prefabs. What's that about?
The second thing is a minor thing that occurred in the 1.9.1 versions. The first time(and only once) you click on an object that has a FSM(or the component in the inspector) after you start Unity or after you exit play mode, the preview window gets focus.