Hi,
I had the same problem. An .aspx page with a placeholder, loading an ascx control in code behind.
I replace the <head> section in my aspx page with <head id="headSection" runat="server" >, and now it works.
As the ascx control had an updatepanel, i had to do the loadcontrol in the page-init method.
Hope that will solve your pb.
Gilles