I have a sample ear project consisting of two ejb jars each including a persistence.xml and an orm.xml.

test.ear
+--test-report.jar
+--META-INF
+--persistence.xml
+--orm.xml
+--test-settings.jar
+--META-INF
+--persistence.xml
+--orm.xml

Basically both ejb jars do not depend on each other. In both ejb jars is at least one JPA entity defined which has no references to an entity of the other ejb.jar. In each orm.xml entity annotations are overwritten.

If I try to deploy the EAR I receive the following exception. Hibernate complains that an entity of the first ejb.jar(ReportLevel - persistence-unit-a) is not defined in the persistence unit of the second ejb.jar (persistence-unit-b) which is not defined in the persistence unit of the second ejb.jar:

14:03:50,286 WARN [ServiceController] Problem starting service persistence.units:ear=test-ear-0.3-SNAPSHOT.ear,unitName=persistence-unit-b
org.hibernate.AnnotationException: @OneToOne or @ManyToOne on de.test.Report.levelName references an unknown entity: de.test.ReportLevel
at org.hibernate.cfg.FkSecondPass.doSecondPass(FkSecondPass.java:56)
at org.hibernate.cfg.AnnotationConfiguration.processFkSecondPassInOrder(AnnotationConfiguration.java:428)
at org.hibernate.cfg.AnnotationConfiguration.secondPassCompile(AnnotationConfiguration.java:286)
at org.hibernate.cfg.Configuration.buildMappings(Configuration.java:1115)
at org.hibernate.ejb.Ejb3Configuration.buildMappings(Ejb3Configuration.java:1233)
at org.hibernate.ejb.EventListenerConfigurator.configure(EventListenerConfigurator.java:154)
at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:869)
at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:407)
at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:126)
at org.jboss.ejb3.entity.PersistenceUnitDeployment.start(PersistenceUnitDeployment.java:246)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.ejb3.ServiceDelegateWrapper.startService(ServiceDelegateWrapper.java:103)
at org.jboss.system.ServiceMBeanSupport.jbossInternalStart(ServiceMBeanSupport.java:289)
at org.jboss.system.ServiceMBeanSupport.jbossInternalLifecycle(ServiceMBeanSupport.java:245)
at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.system.ServiceController$ServiceProxy.invoke(ServiceController.java:978)
at $Proxy0.start(Unknown Source)
at org.jboss.system.ServiceController.start(ServiceController.java:417)
at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)
at $Proxy57.start(Unknown Source)
at org.jboss.ejb3.JmxKernelAbstraction.install(JmxKernelAbstraction.java:120)
at org.jboss.ejb3.Ejb3Deployment.startPersistenceUnits(Ejb3Deployment.java:627)
at org.jboss.ejb3.Ejb3Deployment.start(Ejb3Deployment.java:351)
at org.jboss.ejb3.Ejb3Module.startService(Ejb3Module.java:91)
at org.jboss.system.ServiceMBeanSupport.jbossInternalStart(ServiceMBeanSupport.java:289)
at org.jboss.system.ServiceMBeanSupport.jbossInternalLifecycle(ServiceMBeanSupport.java:245)
at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.system.ServiceController$ServiceProxy.invoke(ServiceController.java:978)
at $Proxy0.start(Unknown Source)
at org.jboss.system.ServiceController.start(ServiceController.java:417)
at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)
at $Proxy33.start(Unknown Source)
at org.jboss.ejb3.EJB3Deployer.start(EJB3Deployer.java:512)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java:133)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOperationInterceptor.java:142)
at org.jboss.mx.interceptor.DynamicInterceptor.invoke(DynamicInterceptor.java:97)
at org.jboss.system.InterceptorServiceMBeanSupport.invokeNext(InterceptorServiceMBeanSupport.java:238)
at org.jboss.wsf.container.jboss42.DeployerInterceptor.start(DeployerInterceptor.java:87)
at org.jboss.deployment.SubDeployerInterceptorSupport$XMBeanInterceptor.start(SubDeployerInterceptorSupport.java:188)
at org.jboss.deployment.SubDeployerInterceptor.invoke(SubDeployerInterceptor.java:95)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)
at $Proxy34.start(Unknown Source)
at org.jboss.deployment.MainDeployer.start(MainDeployer.java:1025)
at org.jboss.deployment.MainDeployer.start(MainDeployer.java:1015)
at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:819)
at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:782)
at sun.reflect.GeneratedMethodAccessor21.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java:133)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOperationInterceptor.java:142)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)
at $Proxy9.deploy(Unknown Source)
at org.jboss.deployment.scanner.URLDeploymentScanner.deploy(URLDeploymentScanner.java:421)
at org.jboss.deployment.scanner.URLDeploymentScanner.scan(URLDeploymentScanner.java:634)
at org.jboss.deployment.scanner.AbstractDeploymentScanner$ScannerThread.doScan(AbstractDeploymentScanner.java:263)
at org.jboss.deployment.scanner.AbstractDeploymentScanner.startService(AbstractDeploymentScanner.java:336)
at org.jboss.system.ServiceMBeanSupport.jbossInternalStart(ServiceMBeanSupport.java:289)
at org.jboss.system.ServiceMBeanSupport.jbossInternalLifecycle(ServiceMBeanSupport.java:245)
at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.system.ServiceController$ServiceProxy.invoke(ServiceController.java:978)
at $Proxy0.start(Unknown Source)
at org.jboss.system.ServiceController.start(ServiceController.java:417)
at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)
at $Proxy4.start(Unknown Source)
at org.jboss.deployment.SARDeployer.start(SARDeployer.java:302)
at org.jboss.deployment.MainDeployer.start(MainDeployer.java:1025)
at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:819)
at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:782)
at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:766)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)
at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)
at org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java:133)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOperationInterceptor.java:142)
at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)
at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)
at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)
at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)
at $Proxy5.deploy(Unknown Source)
at org.jboss.system.server.ServerImpl.doStart(ServerImpl.java:482)
at org.jboss.system.server.ServerImpl.start(ServerImpl.java:362)
at org.jboss.Main.boot(Main.java:200)
at org.jboss.Main$1.run(Main.java:508)
at java.lang.Thread.run(Thread.java:619)
14:03:50,536 INFO [EJB3Deployer] Deployed: file:/C:/applications/jboss-4.2.2.GA/server/default/tmp/deploy/tmp60216test-ear-0.3-SNAPSHOT.ear-contents/test-settings-0.3-SNAPSHOT.jar
14:03:50,536 INFO [EARDeployer] Started J2EE application: file:/C:/applications/jboss-4.2.2.GA/server/default/deploy/test-ear-0.3-SNAPSHOT.ear
14:03:50,536 ERROR [URLDeploymentScanner] Incomplete Deployment listing:

— MBeans waiting for other MBeans —
ObjectName: persistence.units:ear=test-ear-0.3-SNAPSHOT.ear,unitName=persistence-unit-b
State: FAILED
Reason: org.hibernate.AnnotationException: @OneToOne or @ManyToOne on de.test.Report.levelName references an unknown entity: de.test.ReportLevel
I Depend On:
jboss.jca:service=DataSourceBinding,name=DefaultDS

— MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM —
ObjectName: persistence.units:ear=test-ear-0.3-SNAPSHOT.ear,unitName=persistence-unit-b
State: FAILED
Reason: org.hibernate.AnnotationException: @OneToOne or @ManyToOne on de.test.Report.levelName references an unknown entity: de.test.ReportLevel
I Depend On:
jboss.jca:service=DataSourceBinding,name=DefaultDS

14:03:51,005 INFO [Http11Protocol] Starting Coyote HTTP/1.1 on http-127.0.0.1-8081
14:03:51,021 INFO [AjpProtocol] Starting Coyote AJP/1.3 on ajp-127.0.0.1-8009
14:03:51,036 INFO [Server] JBoss (MX MicroKernel) [4.2.2.GA (build: SVNTag=JBoss_4_2_2_GA date=200710221139)] Started in 14s:343ms

The exception occurs because when JBoss starts the second ejb.jar it uses the orm.xml of the first ejb.jar. The hibernate entity manager combines the entity classes of the persistence unit and the entity mappings from the orm.xml into one pool before starting the validation. But JBoss led Hibernate read the orm.xml only from the first ejb.jar and uses it for the second, too which is completely wrong.

I'll attach my sample ear project. Just deploy it on your JBoss and it should fail with the same error.