I had this problem a while back, and I ended up not using RegisterClientScriptInclude.
I placed a placeholder in the header of the page, and added the script tag to the placeholder via a HtmlGenericControl.
I'll see if I can find my code and I'll edit my answer with it.
EDIT
I couldn't find my code, so I just re-created it:
<%@ Page Language="C#" AutoEventWireup="true" CodeBehind="Default.aspx.cs" Inherits="WebApplication1._Default" %>
<!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">
<asp:PlaceHolder runat="server" ID="HeadPlaceHolder"></asp:PlaceHolder>
</head>
<body>
...
</body>
</html>
And the Code Behind:
protected void Page_Load(object sender, EventArgs e)
{
HeadPlaceHolder.Controls.Add(/* Your control here */);
}