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I'm having a problem related to this as well. Is it possible for a join to get tripped up in the de-dup process or is that guaranteed to only occur for the mapper entity I query on? I am getting the de-duping if I query on the mapped entity, but if I query on the id of the entity I get the full number of rows I am expecting, as you indicated. However beyond that, even if I query on the distinct id's, I am getting back the full number of rows I expected, thus leading me to believe some other entity's primary key is getting de-duplicated. Is that possible?
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