You seem to have some JPA plugins installed from Juno. You can check this if you open the Console view, select the Host OSGi console from the view's context menu and enter "ss org.eclipse.jpt.jpa.core". The Indigo version of this plugin is 3.0.x. If you have the 3.2.x version, you have installed the Juno JPA plugin which isn't compatible with Hibernate Tools 3.4.x.
The problem happens because the marketplace includes Helios, Indigo and Juno update sites.
The solution is to reinstall Eclipse and install JBoss Tools/Hibernate Tools from the following JBoss Tools update site: http://download.jboss.org/jbosstools/updates/development/indigo/