Are you using AJAX.ASP.NET Update Panels?  The CuteEditor control is not AJAX-Aware, and what you describe sounds like what I've experienced when I load the CuteEditor into view with a partial-page rendering (Async Postback) instead of a full postback.  I don't have a solution for you if you are using AJAX, other than wait for Version 6 with the rest of us.