I’m also running into a similar issue, has there been any development on it?
At runtime I’m able to instantiate agents from prefabs and assign Behaviour Trees that I created in the editor with no issue. If I try to generate a Behaviour Tree at runtime and assign it to my instantiated agent, the agent’s Behaviour Tree is empty. However, if I cache the generated Behaviour Tree elsewhere and inspect it, it has all of the nodes.
I can provide additional information if needed but OP outlined the issue I’m seeing pretty well.