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Please reopen, this issue still occur with Hibernate 4.1.11.Final (with PostgreSql in my case, but this is not related to a specific database).
In DatabaseMetadata, sequences HashSet still use unqualified sequence name, so if you have 2 applications using each their own schema (quite common) : schema1 and schema2, the first one will work as expected but the second one will fail because schema1.hibernate_sequence will be processed as hibernate_sequence, so schema2.hibernate_sequence will never be created.