Now I'm really confused. Seems according to the trace output that the correct log4j.xml is being loaded..
2010-10-26 10:46:56,791 TRACE [org.jboss.classloader.spi.base.BaseClassLoader] (main) BaseClassLoader@78618ac5{vfsfile:/opt/jboss-5.1.0.GA/server/default/deploy/pentaho.ear/pentaho.war/} getResource log4j.xml domain=ClassLoaderDomain@30e6ace7{pentaho.war}
2010-10-26 10:46:56,791 TRACE [org.jboss.classloader.spi.base.BaseClassLoaderDomain] (main) ClassLoaderDomain@30e6ace7{pentaho.war} trying to get resource log4j.xml from requesting BaseClassLoader@78618ac5{vfsfile:/opt/jboss-5.1.0.GA/server/default/deploy/pentaho.ear/pentaho.war/}
2010-10-26 10:46:56,791 TRACE [org.jboss.classloader.spi.base.BaseClassLoader] (main) BaseClassLoader@78618ac5{vfsfile:/opt/jboss-5.1.0.GA/server/default/deploy/pentaho.ear/pentaho.war/} get resource locally log4j.xml
2010-10-26 10:46:56,797 TRACE [org.jboss.classloader.spi.base.BaseClassLoader] (main) BaseClassLoader@78618ac5{vfsfile:/opt/jboss-5.1.0.GA/server/default/deploy/pentaho.ear/pentaho.war/} got resource locally log4j.xml
Now I am lost as to why log4j is acting as if it has been given a different config. I need to think of a way of isolating this to show exactly what's happening.
Thanks for you help, Ales!