We've just upgraded to Unity 5.3 and PlayMaker appears to be no longer work correctly.
To reproduce:
-Create a GameObject and call it "FSM"
-Create a Cube, Sphere and Plane and spread them apart
-Add an FSM component to the "FSM" GameObject
-Add a LeanTween "Move" component to the first node and set the Cube to move to the Sphere
-Hit Play
-Modify the LeanTween "Move" component and set the Cube to move to the Plane
-Observe that the Cube still moves to the Sphere
This appears to be the same for all PlayMaker nodes - the inspector loses references every single time. We've copied the same project back to 5.1.1 and the same doesn't appear to happen.