Hi
Im having the same kind of problem. I have build up a scene with a player, health_manager, ammo_manager, enemies, bullets etc. It all works perfect.
When the enemies find the player they shoot and decrese his health.
So i made a prefab of the enemie, and a FSM script to tell when and were the prefabs of the enemie will be spawned. And they do spawn. But there FSM script has forgot most of the gameobjects and all variabels they were told to interact with.
I solved there loss of gameobject by simply make a prefab of each gameobject that interact with the enemie, and drag droped each of them into the enemie prefab FSM trought the project panel. So no it dont forget the gameobjects, witch it does if they are drag droped from the hierachy panel.
But i cant solve it with the variabels sense i cant turn them into prefabs
Another thing that is extremly frustating is that when the enemie prefab is shooting at the player, its FSM send a messegae to another FSM within the health_manager and tells it to fire of a dec health event (lower players health), only problem is that the health manager wont fire of the event, even tou its told to do so. If i then replace the prefab with the exact same enmie but not a prefab, it all works great.
i also get this error/ warning (yellow icon) message while run the scene:
DebugFlow: Missing Cached Variables...
UnityEngine.Debug:LogWarning(Object)
HutongGames.PlayMakerEditor.DebugFlow:Stop()
HutongGames.PlayMakerEditor.FsmEditor:PlaymodeChanged()
UnityEditor.Toolbar:OnGUI()
Does anyone know how i can get pass this? somehow i have to. I mean i can not possible add 64 enimies at once to each scene, i need prefabs. :/