I do not use hibernate plugin for eclipse, but <hibernatetool> AND task.
However, I think that your problem is due to the fact that you generate
both .hbm.xml files and .java files (pojos) at the same time reading the
database metadata. Instead of generating mapping files first (.hbm.xml),
add the <meta> tags that you wish (see
http://www.hibernate.org/hib_docs/tools/reference/en/html/codegen.html#d0e2013)
and then generate pojo files from .hbm.xml files using the hibernate.cfg.xml.
I hope this can help you.
regards,
emmie