Thanks for reporting this issue. I have found the cause of this.
To fix this, please open up GraphOwner.cs, find and completely replace the method called “OnGraphSerialized” with the following code:
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//Called in editor only after assigned graph is serialized.
//If the graph is bound, we store the serialization data here.
As you can tell, the cause was calling SetDirty without first checking if something is actually changed. Making this change should resolve the issue, but please let me know if not.