The version mismatch does not seem to be the cause of your duplicate import error, but it certainly is a problem that must be dealt with as the mapping process is slightly different for Hibernate 2 and Hibernate 3 projects. The mapping files created will also have Hibernate 2 DTDs.
Are you sure you selected Hibernate 3 when adding support, do you see this problem with both your original project and the new project? Can you try creating a dummy project with only Hibernate 3 and mapping just a couple of tables so that your test set is smaller?
Can you answer all the relevant questions asked here which you haven’t already answered: Posting Guidelines
Best,
Brian.