Can you please share your "$PROFILE/deploy/jboss-logging.xml" file with us? (Were you having any additional configuration in your Old JBoss5 jboss-log4j.xml file)
Also let us know if you are placing any "log4j.xml" or log4j.properties" file inside your application? If yes, then can you please share it ?
Are you packaging any "log4j.jar" file inside your application?
I recommend to not migrate to JBossAS6, this is a quite old version and not maintained. Or do you mean the EAP6, which is the supported Enterprise version?
If you want to stay with the community edition I would recommend to use WildFly 8 or later.
This will be different to JBossAS but there are a lot benefits and you are on a more up-to-date version then.