When both @Startup annotation and <init-on-startup>true</init-on-startup> in ejb-jar.xml are configured for bean,  "description.getModuleDescription().registerStartupBean()" is called twice in StartupMergingProcessor#handleAnnotations() and in StartupMergingProcessor#handleDeploymentDescriptor(). 

This makes the startup countdown (startupBeansCount in EEModuleDescription) have a wrong value (actual bean count + 1). This causes the count down never reaches 0 and EJB invocation awaits forever.

---------------------------------------------------------

 * ejb3/src/main/java/org/jboss/as/ejb3/deployment/processors/merging/AbstractMergingProcessor.java

~~~
 81     private void processComponentConfig(final DeploymentUnit deploymentUnit, final EEApplicationClasses applicationClasses, final Module module, final DeploymentReflectionIndex deploymentReflectionIndex, final T description) throws DeploymentUnitProcessingException {
 82 
 83         final Class<?> componentClass;
 84         try {
 85             componentClass = module.getClassLoader().loadClass(description.getEJBClassName());
 86         } catch (ClassNotFoundException e) {
 87             throw MESSAGES.failToLoadEjbClass(description.getEJBClassName(),e);
 88         }
 89 
 90         if (!MetadataCompleteMarker.isMetadataComplete(deploymentUnit)) {
 91             handleAnnotations(deploymentUnit, applicationClasses, deploymentReflectionIndex, componentClass, description);
 92         }
 93         handleDeploymentDescriptor(deploymentUnit, deploymentReflectionIndex, componentClass, description);
 94     }
~~~

 * ejb3/src/main/java/org/jboss/as/ejb3/deployment/processors/merging/StartupMergingProcessor.java 

~~~
 46     @Override
 47     protected void handleAnnotations(final DeploymentUnit deploymentUnit, final EEApplicationClasses applicationClasses, final DeploymentReflectionIndex deploymentReflectionIndex, final Class<?> componentClass, final SingletonComponentDescription description) throws DeploymentU    nitProcessingException {
 48         EEModuleClassDescription clazz = applicationClasses.getClassByName(componentClass.getName());
 49         if (clazz != null) {
 50             final ClassAnnotationInformation<Startup, Object> data = clazz.getAnnotationInformation(Startup.class);
 51             if (data != null) {
 52                 if (!data.getClassLevelAnnotations().isEmpty()) {
 53                     description.initOnStartup();
 54                     description.getModuleDescription().registerStartupBean();
 55                 }
 56             }
 57         }
 58     }
 59 
 60     @Override
 61     protected void handleDeploymentDescriptor(final DeploymentUnit deploymentUnit, final DeploymentReflectionIndex deploymentReflectionIndex, final Class<?> componentClass, final SingletonComponentDescription description) throws DeploymentUnitProcessingException {
 62         SessionBeanMetaData data = description.getDescriptorData();
 63         if (data instanceof SessionBean31MetaData) {
 64             SessionBean31MetaData singletonBeanMetaData = (SessionBean31MetaData) data;
 65             Boolean initOnStartup = singletonBeanMetaData.isInitOnStartup();
 66             if (initOnStartup != null && initOnStartup) {
 67                 description.initOnStartup();
 68                 description.getModuleDescription().registerStartupBean();
 69             }
 70         }
 71     }
~~~

 * ee/src/main/java/org/jboss/as/ee/component/EEModuleDescription.java

~~~
308     public int getStartupBeansCount() {
309         return this.startupBeansCount;
310     }
311 
312     public int registerStartupBean() {
313         return ++this.startupBeansCount;
314     }
~~~

I think StartupMergingProcessor#handleDeploymentDescriptor() should skip a processing if it's already marked as InitOnStartup by StartupMergingProcessor#handleAnnotations().

So, I suggest that StartupMergingProcessor#handleDeploymentDescriptor() should check SingletonComponentDescription#isInitOnStartup() before continuing the processing. 

As far as I did a simple test (running the attached reproducer), the following patch can fix the issue: 

~~~
diff --git a/ejb3/src/main/java/org/jboss/as/ejb3/deployment/processors/merging/StartupMergingProcessor.java b/ejb3/src/main/java/org/jboss/as/ejb3/deployment/processors/merging/StartupMergingProcessor.java
index 5e1937f..7fc0d84 100644
--- a/ejb3/src/main/java/org/jboss/as/ejb3/deployment/processors/merging/StartupMergingProcessor.java
+++ b/ejb3/src/main/java/org/jboss/as/ejb3/deployment/processors/merging/StartupMergingProcessor.java
@@ -59,13 +59,17 @@ public class StartupMergingProcessor extends AbstractMergingProcessor<SingletonC
 
     @Override
     protected void handleDeploymentDescriptor(final DeploymentUnit deploymentUnit, final DeploymentReflectionIndex deploymentReflectionIndex, final Class<?> componentClass, final SingletonComponentDescription description) throws DeploymentUnitProcessingException {
-        SessionBeanMetaData data = description.getDescriptorData();
-        if (data instanceof SessionBean31MetaData) {
-            SessionBean31MetaData singletonBeanMetaData = (SessionBean31MetaData) data;
-            Boolean initOnStartup = singletonBeanMetaData.isInitOnStartup();
-            if (initOnStartup != null && initOnStartup) {
-                description.initOnStartup();
-                description.getModuleDescription().registerStartupBean();
+        if (description.isInitOnStartup()) {
+            // Skip. This is already marked as InitOnStartup by @Startup annotation.
+        } else {
+            SessionBeanMetaData data = description.getDescriptorData();
+            if (data instanceof SessionBean31MetaData) {
+                SessionBean31MetaData singletonBeanMetaData = (SessionBean31MetaData) data;
+                Boolean initOnStartup = singletonBeanMetaData.isInitOnStartup();
+                if (initOnStartup != null && initOnStartup) {
+                    description.initOnStartup();
+                    description.getModuleDescription().registerStartupBean();
+                }
             }
         }
     }
~~~

Created attachment 1190307 [details]
BZ1366526-potential-patch.diff

Sorry to forget to mention information about a workaround.

### Workaround

 - Don't use both @Startup annotation and <init-on-startup> in ejb-jar.xml to configure a singleton Startup beans
 - Specify either @Startup annotation or <init-on-startup>.

(In reply to Masafumi Miura from comment #4)
> Sorry to forget to mention information about a workaround.
> 
> ### Workaround
> 
>  - Don't use both @Startup annotation and <init-on-startup> in ejb-jar.xml
> to configure a singleton Startup beans
>  - Specify either @Startup annotation or <init-on-startup>.

Thank you!
This should be fine.

EAP6 PR: https://github.com/jbossas/jboss-eap/pull/2830

Verified with EAP 6.4.11.CP.CR1

Retroactively bulk-closing issues from released EAP 6.4 cummulative patches.