Were you ever able to come up with a resolution to this issue? I'm experiencing a similar issue with a Python script inserting records into a related table. When inverting a selection of all records from the source->destination, the expected result would be only values which are Null or have a non-existent key, but I'm getting results that do exist in the parent feature class. With respect to Richard's reply, I do build a dictionary with the SearchCursors and then insert from the dictionary, so that is not the issue in my case, or yours, I suspect.
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