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The problem you are running into is in fact equals/hashCode problems during loading the Map. The problem is the MapKey and it's use of MapValue in its equals and hashCode calculations. In your situation the equals and hashCodes for MapKey end up changing while it is "in" the Map.
This is confounded by the fact that Hibernate is putting these entries into the map before they are fully initialized. I made a small change here "queue up" the additions until after the ResultSet is done being processed which helps in your case.
But overriding equals and hashCode is always going to leave you open to possible problems unless you are very careful.