Just spent an hour tracking this down in my project...
I was using a 'Set FSM Bool' action, and had selected a global gameobject variable from the dropdown, plus the FSM name and Variable name. It should have worked - but just wouldn't.
I then changed it from a global gameobject on the dropdown, and dragged my target gameobject onto the action. It then worked.
I can't see that anything was setup incorrectly. My gameobject was assigned in the playmaker global window (and was fine during runtime), and it could find it - and give me my FSM/variables.
So I'm guessing this action doesn't fully work as intended.