Yes, that's the problem I had, for sure. I stuck in the following JavaScript code and it's been working fine. My theory is that the fact that I'm dynamically loading all of this inside of a User Control is causing CuteEditor's JavaScript to miss the client ID of the Editor. Make sure this JavaScript comes after the Editor's XML. Or call setText() from document.onload.
var editorID = [stick in the editor ClientID from the codebehind]<%# this.Editor1.ClientID %><%# this.Editor1.ClientID %>;
function setText()
{
document.getElementById(editorID + "_editBox").innerHTML = document.getElementById(editorID + "_HTMLContent").value;
}
setText();