Hello! I struggle the same problem. Did you manage to fix it? I use pretty old v 2.92 NodeCanvas version and Unity 2019.3.13f1. It is not just easy to update it to v3 due to custom changes in NodeCanvas code, but seems it is the last option.
Sometimes reference.GetType() returns UnityObject type despite in insepector there is linked correct MonoBehaviour-derived object. That happens sometimes with different references in different nodes (tasks) to different objects. Most of the time it happens after doing git pull where comes some changes to graph whic contains node with that reference.
I have tried to delay graph deserealization to Awake/OnEnable stage (move it from threaded OnAfterDeserialize). But it seems quite hard to do.
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