Looks like there's a problem merging the xml metadata and the annotations with respect to the @Startup annotation. Use this ejb-jar.xml as a workaround (I have explicitly added the init-on-startup to true in that xml:
<?xml version="1.0" encoding="UTF-8"?>
<ejb-jar xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/ejb-jar_3_1.xsd"
version="3.1">
<enterprise-beans>
<session>
<ejb-name>StartupBean</ejb-name>
<ejb-class>com.example.services.startup.StartupBean</ejb-class>
<session-type>Singleton</session-type>
<init-on-startup>true</init-on-startup>
<ejb-local-ref>
<ejb-ref-name>ejb/VersionManager</ejb-ref-name>
<local>com.example.services.version.VersionManager</local>
<injection-target>
<injection-target-class>com.example.services.startup.StartupBean</injection-target-class>
<injection-target-name>versionManager</injection-target-name>
</injection-target>
<lookup-name>${services.loader}/VersionManagerBean/local</lookup-name>
</ejb-local-ref>
</session>
</enterprise-beans>
</ejb-jar>
Could you please create a JIRA here https://jira.jboss.org/browse/JBMETA about the @Startup issue and point to this thread?