I'm basically only using it for editing static html code inside a contentPlaceHolder (aspx pages). The pages I edit look like this
<%@ Page Language="VB" MasterPageFile="~/MasterPage.master" Title="Name of page" %>
<asp:Content ID="Content1" ContentPlaceHolderID="ContentPlaceHolder1" Runat="Server">
<p>Content I edit here</p>
</asp:Content>
If I add Editor.AllowEditServerSideCode = true nothing is rendered in wysiwig or preview mode in cuteeditor.
As I set it only happens occasionally that the <%@ Page Language="VB" MasterPageFile="~/MasterPage.master" Title="Name of page" %> is removed after editing in cuteeditor.