I have had the same problem and it appears to happen with any kind of link that is a type of "Other".  If the url for your editor location is www.something.com/editor.aspx and you set up a link to Top (to use the existing example).  It will render as <a href="#top">Top</a> just like it should, but if you go back and try to modify the link it will change to <a href="www.something.com/editor.aspx#top">Top</a>.  It seems to want to automatically plug in the page that the editor is on instead of the url/name of the page that is being edited, I have also seen it happen on relative links too.  Hope this helps.