This is a really strange problem. Everything works great as long as I do not change the log4j settings. If I add the following line:

<category name="org.jboss">
<priority value="TRACE" class="org.jboss.logging.XLevel"/>
</category>

Some ejb-links cannot be resolved and are replaced by others.

This is correct:
java:comp namespace of the PublishingBean bean:

+- HandleDelegate (class: org.jboss.proxy.ejb.handle.HandleDelegateImpl)
+- ORB (class: org.jacorb.orb.ORB)
+- env (class: org.jnp.interfaces.NamingContext)

This happens when I turn on trace:

+- HandleDelegate (class: org.jboss.proxy.ejb.handle.HandleDelegateImpl)
+- ORB (class: org.jacorb.orb.ORB)
+- env (class: org.jnp.interfaces.NamingContext)

Additionally I see the following Warnings during deployment:
11:39:56,060 WARN [EjbUtil] LocalHome jndi name requested for: 'QueueProxy' but there is no LocalHome class
11:39:56,060 WARN [EjbUtil] LocalHome jndi name requested for: 'TransactionWriterBean' but there is no LocalHome class
11:39:56,060 WARN [EjbUtil] LocalHome jndi name requested for: 'TPSProxy' but there is no LocalHome class
11:39:56,060 WARN [EjbUtil] LocalHome jndi name requested for: 'PublishProxy' but there is no LocalHome class
11:39:56,069 WARN [EjbUtil] LocalHome jndi name requested for: 'QueueProxy' but there is no LocalHome class
11:39:56,069 WARN [EjbUtil] LocalHome jndi name requested for: 'TransactionWriterBean' but there is no LocalHome class
11:39:56,069 WARN [EjbUtil] LocalHome jndi name requested for: 'TPSProxy' but there is no LocalHome class
11:39:56,069 WARN [EjbUtil] LocalHome jndi name requested for: 'PublishProxy' but there is no LocalHome class
11:39:56,077 WARN [EjbUtil] LocalHome jndi name requested for: 'QueueProxy' but there is no LocalHome class
11:39:56,077 WARN [EjbUtil] LocalHome jndi name requested for: 'TransactionWriterBean' but there is no LocalHome class
11:39:56,078 WARN [EjbUtil] LocalHome jndi name requested for: 'TPSProxy' but there is no LocalHome class
11:39:56,078 WARN [EjbUtil] LocalHome jndi name requested for: 'PublishProxy' but there is no LocalHome class

These are all MDB's so that is of course no home interface.

I also see the following in the server.log

004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] Resolving absolute link, di: org.jboss.deployment.DeploymentInfo@6e24014a

{ url= file:/export/home/mkopp/Server/jboss-4.0.1RC1/server/default/tmp/deploy/tmp18608ftisoft.app.ear-contents/ftisoft.core-ejb.jar }

deployer: org.jboss.ejb.EJBDeployer@f20434
status: Deployed
state: STARTED
watch: file:/export/home/mkopp/Server/jboss-4.0.1RC1/server/default/tmp/deploy/tmp18608ftisoft.app.ear-contents/ftisoft.core-ejb.jar
altDD: null
lastDeployed: 1102415974788
lastModified: 1102415968000
mbeans:
jboss.j2ee:jndiName=ejb/MessagePumpBean,service=EJB state: Started
jboss.j2ee:jndiName=ejb/FileProcessorBean,service=EJB state: Started
jboss.j2ee:jndiName=ejb/StreetLampBean,service=EJB state: Started
jboss.j2ee:jndiName=ejb/FileRestartBean,service=EJB state: Started
jboss.j2ee:jndiName=ejb/local/QueueKeyStreamerBean,service=EJB state: Started
jboss.j2ee:jndiName=ejb/local/TopicKeyStreamerBean,service=EJB state: Started
jboss.j2ee:jndiName=ejb/TransactionProcessorBean,service=EJB state: Started
jboss.j2ee:jndiName=local/QueueProxy,service=EJB state: Started
jboss.j2ee:jndiName=local/TransactionWriterBean,service=EJB state: Started
jboss.j2ee:jndiName=local/TPSProxy,service=EJB state: Started
jboss.j2ee:jndiName=local/PublishProxy,service=EJB state: Started
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] No match for ejb-link: EMailDestination
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/MessagePumpBean
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/FileProcessorBean
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/StreetLampBean
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/FileRestartBean
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/QueueKeyStreamerBean
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/TopicKeyStreamerBean
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/TransactionProcessorBean
2004-12-07 11:39:56,060 WARN [org.jboss.ejb.EjbUtil] LocalHome jndi name requested for: 'QueueProxy' but there is no LocalHome class
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: null
2004-12-07 11:39:56,060 WARN [org.jboss.ejb.EjbUtil] LocalHome jndi name requested for: 'TransactionWriterBean' but there is no LocalHome class
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: null
2004-12-07 11:39:56,060 WARN [org.jboss.ejb.EjbUtil] LocalHome jndi name requested for: 'TPSProxy' but there is no LocalHome class
2004-12-07 11:39:56,060 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: null
2004-12-07 11:39:56,060 WARN [org.jboss.ejb.EjbUtil] LocalHome jndi name requested for: 'PublishProxy' but there is no LocalHome class
2004-12-07 11:39:56,061 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: null
2004-12-07 11:39:56,061 TRACE [org.jboss.mx.interceptor.ModelMBeanAttributeInterceptor] Getting objectName=jboss.j2ee:jndiName=ejb/LogWriterBean,service=EJB attr=
StateString
2004-12-07 11:39:56,061 TRACE [org.jboss.mx.interceptor.ModelMBeanAttributeInterceptor] Removing any cached value objectName=jboss.j2ee:jndiName=ejb/LogWriterBean
,service=EJB attr=StateString descriptor=getMethod=getStateString, currencyTimeLimit=-1, descriptorType=attribute, name=StateString, displayName=StateString
2004-12-07 11:39:56,061 TRACE [org.jboss.mx.interceptor.ModelMBeanAttributeInterceptor] Get attribute objectName=jboss.j2ee:jndiName=ejb/LogWriterBean,service=EJB
attr=StateString getMethod=getStateString
2004-12-07 11:39:56,061 TRACE [org.jboss.mx.interceptor.ModelMBeanAttributeInterceptor] Got attribute objectName=jboss.j2ee:jndiName=ejb/LogWriterBean,service=EJB
attr=StateString value=Started
2004-12-07 11:39:56,061 TRACE [org.jboss.ejb.EjbUtil] Resolving absolute link, di: org.jboss.deployment.DeploymentInfo@2678613

{ url=file:/export/home/mkopp/Serve r/jboss-4.0.1RC1/server/default/tmp/deploy/tmp18608ftisoft.app.ear-contents/ftisoft.process.manager-ejb.jar }

deployer: org.jboss.ejb.EJBDeployer@f20434
status: Deployed
state: STARTED
watch: file:/export/home/mkopp/Server/jboss-4.0.1RC1/server/default/tmp/deploy/tmp18608ftisoft.app.ear-contents/ftisoft.process.manager-ejb.jar
altDD: null
lastDeployed: 1102415975415
lastModified: 1102415969000
mbeans:
jboss.j2ee:jndiName=ejb/LogWriterBean,service=EJB state: Started

2004-12-07 11:39:56,061 TRACE [org.jboss.ejb.EjbUtil] No match for ejb-link: EMailDestination
2004-12-07 11:39:56,061 TRACE [org.jboss.ejb.EjbUtil] ... Has ejbName: ejb/local/LogWriterBean

The one strange thing to see is that the EJB that references the link is in ftisoft.publishing.jar, but the di says ftisoft.core.

One further thing to mention.

There is an MDB inside the ftisoft.core that references the PublishingBean via
<message-driven>
<ejb-name>PublishProxy</ejb-name>
<destination-jndi-name>topic/BEOUT</destination-jndi-name>
<ejb-local-ref >
<ejb-ref-name>ejb/BusinessBean</ejb-ref-name>
<local-jndi-name>ejb/local/PublishingBean</local-jndi-name>
</ejb-local-ref>
</message-driven>

And core seems to get deployed before publish. Could this be an order problem? But why does it work without the trace?