If you check the code below, you will see the client side script src does not have ~ in front of the script path.  the server side (runat=”server”) script path has a ~ in front of the script path.  If the server side omit the ~ , it will still work at runtime, but at design time, it might trigger a javascript intellisense error, so that content of the server side javascript file will not be cached for intellisense.

This is a by design behavior in Visual Studio 2010 RC.  So we just need to remember to follow the correct syntax.

<%@ Page Language="C#" AutoEventWireup="true" CodeFile="Default2.aspx.cs" Inherits="Default2" %>

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">
<head runat="server">
    <title></title>
    <script src="/Scripts/jquery-1.3.2.js" type="text/javascript"></script>
</head>
<body>
    <form id="form1" runat="server">
    <div>
        <asp:ScriptManager ID="ScriptManager1" runat="server">
            <Scripts>
                <asp:ScriptReference Path="~/Scripts/jquery-1.3.2.js" />
            </Scripts>
        </asp:ScriptManager>
    </div>
    </form>
</body>
</html>