Try changing your EJBProcessor configuration to this:
<action class="org.jboss.soa.esb.actions.EJBProcessor" name="callPersist">
<property name="ejb3" value="true" />
<property name="jndi-name" value="garuda-core/ObjShipmentManagerBean/remote-de.eskalon.kn.garuda.api.ObjShipmentManager" />
<property name="initial-context-factory" value="org.jnp.interfaces.NamingContextFactory" />
<property name="provider-url" value="localhost:1099" />
<property name="method" value="persistObjShipment" />
<property name="ejb-params">
<arg0 type="de.eskalon.kn.garuda.database.domain.ObjShipment">get-order-response</arg0>
</property>
</action>
Regards,
/Daniel