Just came here to say that this is a very annoying bug and currently we are looking for workarounds to avoid using Blackboard.
UPDATE
I have investigated into it a bit. When Unity launches Blackboard.SelfDeserialize is called. But at that moment all _objectReferences are null. I think this is because Unity overrides operator == and at the moment referenced prefab is not awaken yet.
UPDATE 2
See my next comment on page 2 of this thread.
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