Hi Bo Sep,
Thank you for using our services.
We have tried to reproduce the issue, however were unable to. Can you please give us a little bit more information about your custom control/template being used. Also are you using Ajax on your page? Is it possible that if this is the case the AjaxManager is set not to update the page header?
Also please check the number of CSS files being loaded on your pages IE explorer has a limit of load ~33 files and all consecutive files are not loaded. If this is the case, please try minimizing the number of CSS files being loaded. For example, you can try using RadStyleSheetManager to combine CSS styles of RadCotnrols, also try combining your CSS files in the theme.
the Telerik team