Cause: The asp.net update panel reloads all the content within the content template tags, thus your custom jquery is not reloaded and never fired.
Solution: Add your custom jquery at the end of the request by using the page request manager object:
var prm = Sys.WebForms.PageRequestManager.getInstance();
prm.add_endRequest(function () {
DOSTUFF();
});
And problem solved, it's as easy as that.
I hope this helped you, it solved my problem.
