JBoss EAP randomly fails to start during automated VM cloning process

Issue

• A template used to clone a complete VM with all services configured include the starting of JBoss Enterprise Application Platform (EAP) results in JBoss randomly failing to start with the following error in boot.log:

ERROR [org.jboss.as.server] JBAS015956: Caught exception during boot: org.jboss.as.controller.persistence.ConfigurationPersistenceException: JBAS014676: Failed to parse configuration
    at org.jboss.as.controller.persistence.XmlConfigurationPersister.load(XmlConfigurationPersister.java:141) [jboss-as-controller-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    at org.jboss.as.server.ServerService.boot(ServerService.java:270) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    at org.jboss.as.controller.AbstractControllerService$1.run(AbstractControllerService.java:156) [jboss-as-controller-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    at java.lang.Thread.run(Thread.java:662) [rt.jar:1.6.0_45]
Caused by: javax.xml.stream.XMLStreamException: JBAS014674: Failed to load module org.jboss.as.security
    at org.jboss.as.controller.parsing.ExtensionXml.parseExtensions(ExtensionXml.java:154) [jboss-as-controller-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    at org.jboss.as.server.parsing.StandaloneXml.readServerElement_1_1(StandaloneXml.java:306) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    at org.jboss.as.server.parsing.StandaloneXml.readElement(StandaloneXml.java:127) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    at org.jboss.as.server.parsing.StandaloneXml.readElement(StandaloneXml.java:99) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    at org.jboss.staxmapper.XMLMapperImpl.processNested(XMLMapperImpl.java:110) [staxmapper-1.1.0.Final-redhat-1.jar:1.1.0.Final-redhat-1]
    at org.jboss.staxmapper.XMLMapperImpl.parseDocument(XMLMapperImpl.java:69) [staxmapper-1.1.0.Final-redhat-1.jar:1.1.0.Final-redhat-1]
    at org.jboss.as.controller.persistence.XmlConfigurationPersister.load(XmlConfigurationPersister.java:133) [jboss-as-controller-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    ... 3 more
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: JBAS014744: No META-INF/services/org.jboss.as.controller.Extension found for org.jboss.as.security:main
    at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222) [rt.jar:1.6.0_45]
    at java.util.concurrent.FutureTask.get(FutureTask.java:83) [rt.jar:1.6.0_45]
    at org.jboss.as.controller.parsing.ExtensionXml.parseExtensions(ExtensionXml.java:146) [jboss-as-controller-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
    ... 9 more
Caused by: java.lang.IllegalStateException: JBAS014744: No META-INF/services/org.jboss.as.controller.Extension found for org.jboss.as.security:main

• The JBoss clone that fails to start by the automated process is able to be successfully started manually.
• strace output shows that sometimes the automated process is encountering empty *.jar.index files, when they should either contain data or not exist.