I have the same problem, and it definately doesn't remove all the extras on the server side.
For example, if I link to an anchor like <a href="#intent"> the editor saves it as:
<a href="http://www.myurl.com.au/CuteSoft_Client/CuteEditor/Template.aspx?Referrer=http%3a%2f%2fwww.myurl.com.au%2fsecure%2fcontent.aspx%3fcontentID%3d80#intent">
THis is causing no end of grief. I've tried setting UseRelativeLinks=true and experimented with disableAutoFormatting and RemoveServerNamesfromURL all to no avail.
Any help would be greatly appreciated!!
Thanks.