Hmm. If you are trying to assign a Blackboard from the same scene, that the GraphOwner prefab Instance is in as well, there should not be any problem . If you were instead trying to assign a Blackboard from the scene, on a GraphOwner prefab Asset (not in the scene), then that will not work since prefab Assets can not have scene object references as usual in Unity.
With that said, I just fixed a potential issue with setting the graphowner prefab dirty and attached the fix for you here. Please import the fix and let me know if that works for you.
Gavalakis
