Injecting a Resource like this
@Resource(mappedName = "java:/JmsXA")
private ConnectionFactory factory;
causes a NPE now in the current trunk version of JBossAS .6.0.0.
A small Test App to reproduce will be added.

This is the complete stacktrace:
13:54:44,372 INFO [org.jboss.ejb3.deployers.Ejb3DependenciesDeployer] Encountered deployment AbstractVFSDeploymentContext@13236330

{vfs:///mbi/tools/jboss/6.00/server/mbi/deploy/test.ear/ejb.jar/}

13:54:44,374 INFO [org.jboss.ejb3.deployers.Ejb3DependenciesDeployer] Encountered deployment AbstractVFSDeploymentContext@13236330

{vfs:///mbi/tools/jboss/6.00/server/mbi/deploy/test.ear/ejb.jar/}

13:54:44,395 INFO [org.jboss.ejb3.instantiator.deployer.BeanInstantiatorDeployerBase] Installed org.jboss.ejb3.instantiator.impl.Ejb31SpecBeanInstantiator@b53bf3 into MC at org.jboss.ejb.bean.instantiator/test/ejb/SessionBean1
13:54:44,397 WARN [org.jboss.ejb3.interceptor.InterceptorInfoRepository] EJBTHREE-1852: InterceptorInfoRepository is deprecated
13:54:44,409 INFO [org.jboss.ejb3.instantiator.deployer.BeanInstantiatorDeployerBase] Uninstalled org.jboss.ejb3.instantiator.impl.Ejb31SpecBeanInstantiator@b53bf3 from MC at org.jboss.ejb.bean.instantiator/test/ejb/SessionBean1
13:54:44,413 ERROR [org.jboss.kernel.plugins.dependency.AbstractKernelController] Error installing to Real: name=vfs:///mbi/tools/jboss/6.00/server/mbi/deploy/test.ear state=PreReal mode=Manual requiredState=Real: org.jboss.deployers.spi.DeploymentException: Error deploying ejb.jar: failed to initialize bean container
at org.jboss.ejb3.deployers.Ejb3Deployer.deploy(Ejb3Deployer.java:191) [:6.0.0-SNAPSHOT]
at org.jboss.ejb3.deployers.Ejb3Deployer.deploy(Ejb3Deployer.java:60) [:6.0.0-SNAPSHOT]
at org.jboss.deployers.vfs.spi.deployer.AbstractSimpleVFSRealDeployer.deploy(AbstractSimpleVFSRealDeployer.java:56) [:2.2.0.Alpha8]
at org.jboss.deployers.spi.deployer.helpers.AbstractSimpleRealDeployer.internalDeploy(AbstractSimpleRealDeployer.java:62) [:2.2.0.Alpha8]
at org.jboss.deployers.spi.deployer.helpers.AbstractRealDeployer.deploy(AbstractRealDeployer.java:55) [:2.2.0.Alpha8]
at org.jboss.deployers.plugins.deployers.DeployerWrapper.deploy(DeployerWrapper.java:179) [:2.2.0.Alpha8]
at org.jboss.deployers.plugins.deployers.DeployersImpl.doDeploy(DeployersImpl.java:1832) [:2.2.0.Alpha8]
at org.jboss.deployers.plugins.deployers.DeployersImpl.doInstallParentFirst(DeployersImpl.java:1550) [:2.2.0.Alpha8]
at org.jboss.deployers.plugins.deployers.DeployersImpl.doInstallParentFirst(DeployersImpl.java:1603) [:2.2.0.Alpha8]
at org.jboss.deployers.plugins.deployers.DeployersImpl.install(DeployersImpl.java:1491) [:2.2.0.Alpha8]
at org.jboss.dependency.plugins.AbstractControllerContext.install(AbstractControllerContext.java:379) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:2044) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.dependency.plugins.AbstractController.incrementState(AbstractController.java:1083) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.dependency.plugins.AbstractController.executeOrIncrementStateDirectly(AbstractController.java:1322) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1246) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1139) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:939) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:654) [jboss-dependency.jar:2.2.0.Alpha10]
at org.jboss.deployers.plugins.deployers.DeployersImpl.change(DeployersImpl.java:1983) [:2.2.0.Alpha8]
at org.jboss.deployers.plugins.deployers.DeployersImpl.process(DeployersImpl.java:1076) [:2.2.0.Alpha8]
at org.jboss.deployers.plugins.main.MainDeployerImpl.process(MainDeployerImpl.java:679) [:2.2.0.Alpha8]
at org.jboss.system.server.profileservice.deployers.MainDeployerPlugin.process(MainDeployerPlugin.java:106) [:6.0.0-SNAPSHOT]
at org.jboss.profileservice.dependency.ProfileControllerContext$DelegateDeployer.process(ProfileControllerContext.java:130) [:0.1.0.Alpha1]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner$HDScanAction.deploy(HDScanner.java:240) [:0.1.0.Alpha1]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner$HDScanAction.complete(HDScanner.java:192) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.TwoPCActionWrapper.doComplete(TwoPCActionWrapper.java:59) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.actions.AbstractTwoPhaseModificationAction.complete(AbstractTwoPhaseModificationAction.java:74) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.actions.AbstractTwoPhaseModificationAction.prepare(AbstractTwoPhaseModificationAction.java:94) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.ModificationSession.prepare(ModificationSession.java:87) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.AbstractActionController.internalPerfom(AbstractActionController.java:234) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.AbstractActionController.performWrite(AbstractActionController.java:213) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.AbstractActionController.perform(AbstractActionController.java:150) [:0.1.0.Alpha1]
at org.jboss.profileservice.management.AbstractActionController.perform(AbstractActionController.java:135) [:0.1.0.Alpha1]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner.scan(HDScanner.java:146) [:0.1.0.Alpha1]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner.run(HDScanner.java:90) [:0.1.0.Alpha1]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) [:1.6.0_22]
at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:317) [:1.6.0_22]
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:150) [:1.6.0_22]
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$101(ScheduledThreadPoolExecutor.java:98) [:1.6.0_22]
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.runPeriodic(ScheduledThreadPoolExecutor.java:180) [:1.6.0_22]
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:204) [:1.6.0_22]
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [:1.6.0_22]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [:1.6.0_22]
at java.lang.Thread.run(Thread.java:662) [:1.6.0_22]
Caused by: java.lang.RuntimeException: failed to initialize bean container
at org.jboss.ejb3.EJBContainer.<init>(EJBContainer.java:304) [:1.6.3]
at org.jboss.ejb3.TimerServiceContainer.<init>(TimerServiceContainer.java:86) [:1.6.3]
at org.jboss.ejb3.session.SessionContainer.<init>(SessionContainer.java:124) [:1.6.3]
at org.jboss.ejb3.session.SessionSpecContainer.<init>(SessionSpecContainer.java:94) [:1.6.3]
at org.jboss.ejb3.stateless.StatelessContainer.<init>(StatelessContainer.java:116) [:1.6.3]
at org.jboss.ejb3.Ejb3AnnotationHandler.getStatelessContainer(Ejb3AnnotationHandler.java:330) [:1.6.3]
at org.jboss.ejb3.Ejb3DescriptorHandler.getStatelessContainer(Ejb3DescriptorHandler.java:499) [:1.6.3]
at org.jboss.ejb3.Ejb3AnnotationHandler.getContainers(Ejb3AnnotationHandler.java:211) [:1.6.3]
at org.jboss.ejb3.Ejb3Deployment.deployElement(Ejb3Deployment.java:771) [:1.6.3]
at org.jboss.ejb3.Ejb3Deployment.deployElement(Ejb3Deployment.java:722) [:1.6.3]
at org.jboss.ejb3.Ejb3Deployment.deployUrl(Ejb3Deployment.java:704) [:1.6.3]
at org.jboss.ejb3.Ejb3Deployment.deploy(Ejb3Deployment.java:667) [:1.6.3]
at org.jboss.ejb3.Ejb3Deployment.create(Ejb3Deployment.java:544) [:1.6.3]
at org.jboss.ejb3.deployers.Ejb3Deployer.deploy(Ejb3Deployer.java:177) [:6.0.0-SNAPSHOT]
... 43 more
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 0
at java.lang.String.charAt(String.java:686) [:1.6.0_22]
at org.jboss.ejb3.connectionmanager.CachedConnectionInterceptorFactory.createPerClass(CachedConnectionInterceptorFactory.java:58) [:1.6.3]
at org.jboss.aop.microcontainer.beans.DelegatingBeanAspectFactory.createPerClass(DelegatingBeanAspectFactory.java:96) [jboss-aop-mc-int.jar:2.2.0.Alpha10]
at org.jboss.aop.Advisor.addPerClassAspect(Advisor.java:1274) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.advice.ScopedInterceptorFactory.create(ScopedInterceptorFactory.java:75) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.Advisor.createInterceptorChain(Advisor.java:1328) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.ejb3.interceptors.container.ManagedObjectAdvisor.createInterceptorChain(ManagedObjectAdvisor.java:141) [:1.0.8]
at org.jboss.aop.Advisor.pointcutResolved(Advisor.java:1942) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.MethodMatchInfo.applyBinding(MethodMatchInfo.java:152) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.MethodMatchInfo.overridePopulateBindings(MethodMatchInfo.java:143) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.MethodMatchInfo.populateBindings(MethodMatchInfo.java:92) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.Advisor.finalizeMethodChain(Advisor.java:1553) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.ClassAdvisor.finalizeChains(ClassAdvisor.java:741) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.ClassAdvisor.createInterceptorChains(ClassAdvisor.java:609) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.aop.ClassAdvisor$1.run(ClassAdvisor.java:306) [jboss-aop.jar:2.2.1.Alpha3]
at java.security.AccessController.doPrivileged(Native Method) [:1.6.0_22]
at org.jboss.aop.ClassAdvisor.attachClass(ClassAdvisor.java:276) [jboss-aop.jar:2.2.1.Alpha3]
at org.jboss.ejb3.interceptors.container.ManagedObjectAdvisor.initialize(ManagedObjectAdvisor.java:174) [:1.0.8]
at org.jboss.ejb3.aop.ExtendedManagedObjectAdvisor.initialize(ExtendedManagedObjectAdvisor.java:70) [:1.6.3]
at org.jboss.ejb3.interceptors.container.AbstractContainer.initializeAdvisor(AbstractContainer.java:180) [:1.0.8]
at org.jboss.ejb3.aop.BeanContainer.initialize(BeanContainer.java:193) [:1.6.3]
at org.jboss.ejb3.EJBContainer.<init>(EJBContainer.java:300) [:1.6.3]
... 56 more