Referenced component either it is specified or not should not affect the difference in look of a notification message
Example:
<window id="w" height="100%" width="100%" position="center, center">
<hlayout>
<button onClick='Clients.showNotification("Some Text", Clients.NOTIFICATION_TYPE_WARNING, null, "middle_center", 3000)' label="No referenced component" autodisable="self"/>
<button onClick='Clients.showNotification("Some Text", Clients.NOTIFICATION_TYPE_WARNING, w, "middle_center", 3000)' label="referenced component specified" autodisable="self"/>
</hlayout>
</window>

Discussion of this issue is present on Forum:
http://forum.zkoss.org/question/91938/issue-with-clientshownotification-modal-window/?answer=92470#post-id-92470