For some reasons BeautifulSouf does not convert entities with convertEntities=["xml","html"], use convertEntities=BeautifulSoup.ALL_ENTITIES instead.
{% if flash.message %}
<script type="text/javascript">
<!--
$(function() {
enqueueMsg('{{ flash.message }}');
}) ;
-->
</script>
<div id="t-msg-wrapper" class="message" style="top:30px;left:30px; position:absolute;"></div>
{% endif %}