I have solved this issue as below:
1) The MBean could not locate que EJB in jndi tree because it was not referenced in the mbean declaration as a dependency. So, I did this:
<mbean code="app.SchedulerManager" name="Company:service=SchedulerManager">
<depends>jboss.j2ee:module=my-ejb-jar.jar,service=EjbModule</depends>
</mbean>
2) I also declared the in the META-INF/jboss.xml of the ejb jar so that the dependency can be found:
<jmx-name>jboss.j2ee:module=my-ejb-jar.jar,service=EjbModule</jmx-name>