jUDDI 3 uses Hibernate to access db. During server startup it tries to update db schema to conform mapping files. Unfortunately on Oracle if tables with the same name exists in an other schema then jUDDI thinks that db is correctly initialized and tables are not created.
To fix this issue it is necessary to use hibernate options hibernate.default_schema and/or hibernate.default_catalog in persistence.xml file. This can cuase problems with other databases.
I have tried to change hibernate.hbm2ddl.auto from update to create and issue has disappeared. Moreover this approach is better aligned with other db components using static sql files - no schema change is done inadvertently.