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From what I see in the code, Configuration.MappingsImpl.TableColumnNameBinding.logicalToPhysical map is using unquoted logical column name as key (unless naming strategy is explicitly quoting logical column names, which is not the cases with default naming strategy, and probably should never be the case). Whereas Configuration.buildUniqueKeyFromColumnNames() method, which is using this map to transform user-provided logical column names to physical names, always quotes the logical name before doing the lookup, thus causing the issue.