In Preferences, turn off Auto Load All Prefabs in Project.
I assume you have a large project with a lot of prefabs?
The reason to Auto Load prefabs is to make global changes easier - right now the Playmaker editor only acts on loaded PlayMakerFSMs. I'm looking into optimizing the auto load in a future update.
With Auto Load turned off, PlayMakerFSMs are loaded as you click on the prefabs (the default Unity behavior).
Let me know if that works, or if there's another issue...