Objects structure:

Project<1-*>DataSourceSchema<1-1>VersionedSource<1-1>AbstractSource<1-1>Configuration.
also
Project<1-*>Archive

All the object are JPA entities beside the Configuration object which is a UserType

Workflow
1.create HB session
2. create a project object
3. save project --OK (insert are made into the DB)
4. modify project
5. save project -- here the exception occurs (Found two representations of same collection: Project.archives)
6.close HB session


Hibernate version:
Hibernate 3.2.4

Code between sessionFactory.openSession() and session.close():
public void save(T objectToSave) {
EntityManager em = this.getEntityManager();

if (!em.getTransaction().isActive()) {
em.getTransaction().begin();
}

((Session) em.getDelegate()).saveOrUpdate(objectToSave);

em.getTransaction().commit();
}

Full stack trace of any exception that occurs:
javax.persistence.RollbackException: Error while commiting the transaction
at org.hibernate.ejb.TransactionImpl.commit(TransactionImpl.java:71)
at com.bobj.datafederator.designer.domain.dao.jpa.LocalThreadDataAccess.delete(LocalThreadDataAccess.java:73)
at com.bobj.datafederator.designer.domain.dao.jpa.LocalThreadDataAccess.delete(LocalThreadDataAccess.java:1)
at com.bobj.datafederator.designer.domain.ProjectDaoService.delete(ProjectDaoService.java:99)
at com.bobj.datafederator.designer.domain.ProjectDaoService.deleteAllProjects(ProjectDaoService.java:108)
at com.bobj.datafederator.designer.DfTestCase.deleteAllProjects(DfTestCase.java:64)
at com.bobj.datafederator.designer.DfTestCase.setUp(DfTestCase.java:44)
at junit.framework.TestCase.runBare(TestCase.java:128)
at junit.framework.TestResult$1.protect(TestResult.java:106)
at junit.framework.TestResult.runProtected(TestResult.java:124)
at junit.framework.TestResult.run(TestResult.java:109)
at junit.framework.TestCase.run(TestCase.java:120)
at junit.framework.TestSuite.runTest(TestSuite.java:230)
at junit.framework.TestSuite.run(TestSuite.java:225)
at org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestReference.run(JUnit3TestReference.java:130)
at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
Caused by: org.hibernate.HibernateException: Found two representations of same collection: com.bobj.datafederator.designer.domain.Project.archives
at org.hibernate.engine.Collections.processReachableCollection(Collections.java:153)
at org.hibernate.event.def.FlushVisitor.processCollection(FlushVisitor.java:37)
at org.hibernate.event.def.AbstractVisitor.processValue(AbstractVisitor.java:101)
at org.hibernate.event.def.AbstractVisitor.processValue(AbstractVisitor.java:61)
at org.hibernate.event.def.AbstractVisitor.processEntityPropertyValues(AbstractVisitor.java:55)
at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:131)
at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:196)
at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:76)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:26)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
at org.hibernate.ejb.TransactionImpl.commit(TransactionImpl.java:54)

Name and version of the database you are using:
HSQLDB