I have the tinymce -control as a WYSIWYG-Editior in my asp.net page.
When I have e.g. a Text in Bold, after the Postback it is shown as
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Try passing your js code to the ScriptManager. Worked for me.
string script = "alert('something')"; ScriptManager.RegisterClientScriptBlock(UpdatePanelSend, typeof(UpdatePanel), "jscript", script, true);
http://snippets.dzone.com/posts/show/6725
Hope this helps.