I'm not sure whether this question is still important for you, however I will try to provide a reasonable answer below.
AJAX framework does not evaluate scripts which are returned via UpdatePanel calls. You have to re-attach external scripts to document, so that browser could request for them and evaluate all inline scripts. You can use a small module I have paste below.
var UpdatePanelEnhancer = function ()
{
var divSelector = '#liveArea';
function evaluateScripts()
{
$(divSelector).find('script').each(function ()
{
if (this.src)
{
$('body').append(this);
}
else
{
var content = $(this).html();
eval(content);
}
});
};
Sys.Application.add_load(evaluateScripts);
} ();
The weak part of it is that you have to provide a selector for the element where module should look for a scripts to evaluate ('liveArea' in example), although you can extend the module and provide some cinfiguration to it. Also, I would strongly recommend you to load external javascripts before. If you cannot do it for some reason you should additionally check whether script is already referenced or not to avoid necessary calls and potentially unexpected behaviors and errors .