Ok, so I think I reached a conclusion on this issue. There is not a problem with the combination of these technologies and/or patterns but with the version of Hibernate. I used Hibernate 3 before and the logging went just fine but according to this documentation http://docs.jboss.org/hibernate/orm/4.2/manual/en-US/html/ch03.html#configuration-logging starting with Hibernate 4.0 they gave up on slf4j as the logging facade and they switched to JBoss logging. From this link (https://community.jboss.org/wiki/Logging) it seems that JBoss logging has a variant that uses log4j but unfortunately I haven't managed to configure the whole environment to use JBoss logging instead of slf4j. For my application I reverted to Hibernate 3 and the logging is going just fine.
If there is someone that used Hibernate 4 with JBoss logging and log4j and has some sample configuration I think it would be appreciated by many people as I haven't found any relevant information in my searches.
Thank you for any relevant information you might have.