We have an EAR structured like the following:

It is actually a simple exploded EAR with a single session EJB from the EJB3 tutorial.

The EJB will not deploy.

sample.ear
ejbs
ejbclasses.jar
META-INF
application.xml

The only error is the following:

13:32:22,431 INFO [BeanInstantiatorDeployerBase] Installed org.jboss.ejb3.instantiator.impl.Ejb31SpecBeanInstantiator@7da1fc into MC at org.jboss.ejb.bean.instantiator/simple/ejbs/ejbclasses/CalculatorBean
13:32:22,462 WARN [InterceptorInfoRepository] EJBTHREE-1852: InterceptorInfoRepository is deprecated
13:32:22,821 INFO [JBossASKernel] Created KernelDeployment for: ejbclasses.jar
13:32:22,821 INFO [JBossASKernel] installing bean: jboss.j2ee:ear=simple.ear,jar=ejbclasses.jar,name=CalculatorBean,service=EJB3
13:32:22,821 INFO [JBossASKernel] with dependencies:
13:32:22,821 INFO [JBossASKernel] and demands:
13:32:22,821 INFO [JBossASKernel] jboss.ejb:service=EJBTimerService; Required: Described
13:32:22,821 INFO [JBossASKernel] jboss-switchboard:appName=simple,module=ejbs/ejbclasses,name=CalculatorBean; Required: Create
13:32:22,821 INFO [JBossASKernel] and supplies:
13:32:22,837 INFO [JBossASKernel] Class:org.jboss.tutorial.stateless.bean.CalculatorRemote
13:32:22,837 INFO [JBossASKernel] Class:org.jboss.tutorial.stateless.bean.CalculatorLocal
13:32:22,837 INFO [JBossASKernel] jndi:simple/CalculatorBean/remote-org.jboss.tutorial.stateless.bean.CalculatorRemote
13:32:22,837 INFO [JBossASKernel] jndi:simple/CalculatorBean/local-org.jboss.tutorial.stateless.bean.CalculatorLocal
13:32:22,837 INFO [JBossASKernel] jndi:simple/CalculatorBean/remote
13:32:22,837 INFO [JBossASKernel] jndi:simple/CalculatorBean/local
13:32:22,837 INFO [JBossASKernel] jndi:CalculatorBean
13:32:22,837 INFO [JBossASKernel] Added bean(jboss.j2ee:ear=simple.ear,jar=ejbclasses.jar,name=CalculatorBean,service=EJB3) to KernelDeployment of: ejbclasses.jar
13:32:22,946 INFO [service] Removing bootstrap log handlers
13:32:23,024 ERROR [ProfileServiceBootstrap] Failed to load profile:: org.jboss.deployers.client.spi.IncompleteDeploymentException: Summary of incomplete deployments (SEE PREVIOUS ERRORS FOR DETAILS):

DEPLOYMENTS MISSING DEPENDENCIES:
Deployment "jboss.ejb3:application=simple,module=ejbclasses,component=CalculatorBean,service=EjbEncFactory" is missing the following dependencies:
Dependency "jboss.naming:application=simple,component=CalculatorBean,module=ejbclasses" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'jboss.naming:application=simple,component=CalculatorBean,module=ejbclasses' **")
Deployment "jboss.j2ee:ear=simple.ear,jar=ejbclasses.jar,name=CalculatorBean,service=EJB3" is missing the following dependencies:
Dependency "jboss.ejb3:application=simple,component=CalculatorBean,module=ejbclasses,service=EjbEncFactory" (should be in state "Installed", but is actually in state "Described")
Dependency "org.jboss.ejb.bean.instantiator/simple/ejbclasses/CalculatorBean" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/simple/ejbclasses/CalculatorBean' **")
Deployment "jboss.j2ee:ear=simple.ear,jar=ejbclasses.jar,name=CalculatorBean,service=EJB3_endpoint" is missing the following dependencies:
Dependency "jboss.j2ee:ear=simple.ear,jar=ejbclasses.jar,name=CalculatorBean,service=EJB3" (should be in state "Installed", but is actually in state "Instantiated")

NOTE the module name shown for jboss-switchboard. It is ejbs/ejbclasses and in the dependency errors it is only known as ejbclasses?

If I change the structure to the following the EJB will deploy:

sample.ear
ejbclasses.jar
META-INF
application.xml