Your script references are probably broken because they are relative references and you are using now a virtual directory in IIS.
You need to use the Url.Content
helper method where you can specify your root directory with ~
which will take care of the virtual directories and generates the correct urls for you:
<script src="@Url.Content("~/Scripts/jquery-1.7.1.js")" type="text/javascript">
</script>
<script src="@Url.Content("~/Scripts/knockout-2.1.0.js")" type="text/javascript">
</script>