The problem from converting or upgrading from the 5.3 to the 6.0 version was the fact that you have changed the path and property names, etc. in the CuteEditor. I created my own security config file a few years ago and the property value was...
SecurityPolicyFile
="mypolicyname.config" AutoConfigure="none"
Now I had to use...
ConfigurationPath
="~/CuteSoft_Client/CuteEditor/Configuration/mypolicyname.config"
That was the reason that this code wouldn't work...
CType(oCuteEditor.ToolControls("NewEmail").Control, System.Web.UI.WebControls.WebControl).Attributes.Add("onclick", "return ConfirmNewEmailWindow(""Are you sure you want to clear this email??\nSelect 'OK' to delete or 'Cancel' to quit."",'" & oCuteEditor.ClientID & "');")
By the way, that line of code above is pretty cool. It basically addes an onclick event to a custom button that I defined with a name of NewEmail in my mypolicyname.config file. :)
The problem was because my 'NewEmail' button wasn't loading and because the editor had no config or something, it wasn't really loading! So it would fail. I guess if there are any errors in your HTML configuration settings for the CuteEditor, it goes crazy and doesn't even load. I hope this helps someone else.