When a lot of objects have been resolved in the current transaction, queries becomes slow. see http://www.jboss.com/index.html?module=bb&op=viewtopic&t=68954&postdays=0&postorder=asc&start=0 for more details.

More generally, it seems that EJB3 persistence access is slower in JBoss EJB3 compare to access in EJB3 outside of JBoss:
see http://forum.hibernate.org/viewtopic.php?t=948850