do you have this in navbar under
<!-- / user cp tools menu -->, if not add it.
Code:
<if condition="$notifications_total">
<!-- notifications menu -->
<div class="vbmenu_popup" id="notifications_menu" style="display:none">
<table cellpadding="4" cellspacing="1" border="0">
<tr><td class="thead" colspan="2">$vbphrase[your_notifications]</td></tr>
$notifications_menubits
</table>
</div>
<!-- / notifications menu -->
</if>