Based on url: http://stackoverflow.com/questions/455912/script-script-inside-a-repeater-control-code-not-showing-up-in-the-source-code you are injecting the javascript into the repeater using the code behind.
For testing purposes, can you try placing your script tags within the ItemTemplate?
My second suggestion would be to pass the values required to construct the javascript as part of your datasource and then output them as part of your template:
<script type="text/javascript">
AudioPlayer.embed('<%#DataBinder.Eval(Container.DataItem, "ID")%>', {soundFile: '<%#DataBinder.Eval(Container.DataItem, "Url")%>'});
</script>
Regards
Gavin