I've spent ages trying to work out what was happening to hibernate logging output, when running hibernate apps under Websphere.
Essentially this is because IBM have their own Commons Logging compliant logger, which is what Hibernate gets given when it asks for a Logger from the LogFactory.
So, in order to see any Hibernate logging, you either have to indulge in a fair amount of work reconfiguring Websphere to use something other than its own logger (i.e. Log4J), which you can then configure yourself, or use the Websphere Admin console to configure its internal logging to show Hibernate logging.
It's all explained very well here:
http://www.webspherepower.com/issuespri ... 01281.html
Maybe this should be added to the FAQ (shoot me if it already is!)