I've bundled an EAR with maven-ear-plugin (version 2.5-SNAPSHOT, with Java EE 6 features), where I've set the applicationName to tell how the JNDI tree should give names to EJB's in the application.
Stacktrace:

21:14:29,954 WARN [org.jboss.profileservice.deployment.hotdeploy.HDScanner] Scan failed: org.jboss.deployers.client.spi.IncompleteDeploymentException: Summary of incomplete deployments (SEE PREVIOUS ERRORS FOR DETAILS):

DEPLOYMENTS MISSING DEPENDENCIES:
Deployment "jboss-switchboard:appName=mds,module=mds-console-web-1.1.9-SNAPSHOT" is missing the following dependencies:
Dependency "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MasterDataBean,service=EJB3" (should be in state "Installed", but is actually in state "Instantiated")
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,module=mds-biz-ejb-1.1.9-SNAPSHOT,component=MDDValidatorBean,service=EjbEncFactory" is missing the following dependencies:
Dependency "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MDDValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MDDValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **")
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,module=mds-biz-ejb-1.1.9-SNAPSHOT,component=MasterDataBean,service=EjbEncFactory" is missing the following dependencies:
Dependency "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **")
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,module=mds-biz-ejb-1.1.9-SNAPSHOT,component=MasterDataXMLValidatorBean,service=EjbEncFactory" is missing the following dependencies:
Dependency "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataXMLValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataXMLValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **")
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,module=mds-biz-ejb-1.1.9-SNAPSHOT,component=RbacBean,service=EjbEncFactory" is missing the following dependencies:
Dependency "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=RbacBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=RbacBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MDDValidatorBean,service=EJB3" is missing the following dependencies:
Dependency "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=MDDValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" (should be in state "Installed", but is actually in state "Described")
Dependency "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MDDValidatorBean" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MDDValidatorBean' **")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MDDValidatorBean,service=EJB3_endpoint" is missing the following dependencies:
Dependency "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MDDValidatorBean,service=EJB3" (should be in state "Installed", but is actually in state "Instantiated")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MasterDataBean,service=EJB3" is missing the following dependencies:
Dependency "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataBean" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataBean' **")
Dependency "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" (should be in state "Installed", but is actually in state "Described")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MasterDataBean,service=EJB3_endpoint" is missing the following dependencies:
Dependency "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MasterDataBean,service=EJB3" (should be in state "Installed", but is actually in state "Instantiated")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MasterDataXMLValidatorBean,service=EJB3" is missing the following dependencies:
Dependency "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataXMLValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" (should be in state "Installed", but is actually in state "Described")
Dependency "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataXMLValidatorBean" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataXMLValidatorBean' **")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MasterDataXMLValidatorBean,service=EJB3_endpoint" is missing the following dependencies:
Dependency "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=MasterDataXMLValidatorBean,service=EJB3" (should be in state "Installed", but is actually in state "Instantiated")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=RbacBean,service=EJB3" is missing the following dependencies:
Dependency "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/RbacBean" (should be in state "Installed", but is actually in state "** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/RbacBean' **")
Dependency "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=RbacBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" (should be in state "Installed", but is actually in state "Described")
Deployment "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=RbacBean,service=EJB3_endpoint" is missing the following dependencies:
Dependency "jboss.j2ee:ear=mds-ear-1.1.9-SNAPSHOT.ear,jar=mds-biz-ejb-1.1.9-SNAPSHOT.jar,name=RbacBean,service=EJB3" (should be in state "Installed", but is actually in state "Instantiated")
Deployment "jboss.web.deployment:war=/mds-console-web" is missing the following dependencies:
Dependency "jboss-switchboard:appName=mds,module=mds-console-web-1.1.9-SNAPSHOT" (should be in state "Installed", but is actually in state "Deploy")

DEPLOYMENTS IN ERROR:
Deployment "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/RbacBean" is in error due to the following reason(s): ** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/RbacBean' **
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=MDDValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" is in error due to the following reason(s): Described
Deployment "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataXMLValidatorBean" is in error due to the following reason(s): ** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataXMLValidatorBean' **
Deployment "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MDDValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" is in error due to the following reason(s): ** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MDDValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **
Deployment "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataXMLValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" is in error due to the following reason(s): ** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataXMLValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **
Deployment "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataBean" is in error due to the following reason(s): ** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MasterDataBean' **
Deployment "org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MDDValidatorBean" is in error due to the following reason(s): ** NOT FOUND Depends on 'org.jboss.ejb.bean.instantiator/mds-ear-1.1.9-SNAPSHOT/mds-biz-ejb-1.1.9-SNAPSHOT/MDDValidatorBean' **
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" is in error due to the following reason(s): Described
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataXMLValidatorBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" is in error due to the following reason(s): Described
Deployment "jboss.ejb3:application=mds-ear-1.1.9-SNAPSHOT,component=RbacBean,module=mds-biz-ejb-1.1.9-SNAPSHOT,service=EjbEncFactory" is in error due to the following reason(s): Described
Deployment "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=RbacBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" is in error due to the following reason(s): ** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=RbacBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **
Deployment "jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataBean,module=mds-biz-ejb-1.1.9-SNAPSHOT" is in error due to the following reason(s): ** NOT FOUND Depends on 'jboss.naming:application=mds-ear-1.1.9-SNAPSHOT,component=MasterDataBean,module=mds-biz-ejb-1.1.9-SNAPSHOT' **

at org.jboss.deployers.plugins.deployers.DeployersImpl.checkComplete(DeployersImpl.java:1370) [:2.2.0.GA]
at org.jboss.deployers.plugins.deployers.DeployersImpl.checkComplete(DeployersImpl.java:1316) [:2.2.0.GA]
at org.jboss.deployers.plugins.main.MainDeployerImpl.checkComplete(MainDeployerImpl.java:968) [:2.2.0.GA]
at org.jboss.system.server.profileservice.deployers.MainDeployerPlugin.checkComplete(MainDeployerPlugin.java:82) [:6.0.0.Final]
at org.jboss.profileservice.dependency.ProfileControllerContext$DelegateDeployer.checkComplete(ProfileControllerContext.java:138) [:0.2.2]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner$HDScanAction.deploy(HDScanner.java:246) [:0.2.2]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner$HDScanAction.complete(HDScanner.java:192) [:0.2.2]
at org.jboss.profileservice.management.TwoPCActionWrapper.doComplete(TwoPCActionWrapper.java:57) [:0.2.2]
at org.jboss.profileservice.management.actions.AbstractTwoPhaseModificationAction.complete(AbstractTwoPhaseModificationAction.java:74) [:0.2.2]
at org.jboss.profileservice.management.actions.AbstractTwoPhaseModificationAction.prepare(AbstractTwoPhaseModificationAction.java:95) [:0.2.2]
at org.jboss.profileservice.management.ModificationSession.prepare(ModificationSession.java:87) [:0.2.2]
at org.jboss.profileservice.management.AbstractActionController.internalPerfom(AbstractActionController.java:234) [:0.2.2]
at org.jboss.profileservice.management.AbstractActionController.performWrite(AbstractActionController.java:213) [:0.2.2]
at org.jboss.profileservice.management.AbstractActionController.perform(AbstractActionController.java:150) [:0.2.2]
at org.jboss.profileservice.management.AbstractActionController.perform(AbstractActionController.java:135) [:0.2.2]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner.scan(HDScanner.java:146) [:0.2.2]
at org.jboss.profileservice.deployment.hotdeploy.HDScanner.run(HDScanner.java:90) [:0.2.2]
at java.util.concurrent.Executors$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]

When I remove the applicationName it deploys correctly.

The maven-ear-plugin setup is like this:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-ear-plugin</artifactId>
<configuration>
<defaultLibBundleDir>lib</defaultLibBundleDir>
<generateApplicationXml>true</generateApplicationXml>
<version>6</version> <Unable to render embedded object: File (-- Only applicable when generateApplicationXml is true) not found. (JEE version?!)-->
<applicationName>mds</applicationName>
<jboss>
<version>5</version> <!-- JBoss AS version -->
<library-directory>/lib</library-directory>
<loader-repository>com.tracetracker:loader=${project.build.finalName}.ear</loader-repository>
<loader-repository-config>java2ParentDelegation=false</loader-repository-config>
</jboss>
</configuration>
</plugin>