I've had this problem a few times. It seems to start after a crash and builds into a bigger problem over time.
At first I notice the drop down menu (for game object variable) floats a few 100 pixels above where it should. See attached image.
After some time, the global variables start to have problems. I notice some actions point to the wrong game object global. Two game object variables (for example A and B) get entangled and become unusable (now the variables are listed as A and A). I delete them both and create new ones but other problems start to surface.
Now I have problems with corrupted individual actions. For example, i had a trigger action that wouldn't work until I deleted the action and applied a new one.
I'm afraid I have to rebuild the entire game in a new file. Short of doing that, is there any technique for cleaning global variables or FSMs? When a drop down "remembers" a variable, is there a way to clean out any bad references?
I've recently read Jean mention a playmaker/prefab bug? Maybe this has something to do with that? I am using playmaker with nested prefabs btw.