It seems unlikely that the fault is with the editor, all it is doing is putting text on your page. It is far more likely to be in the css of the page elements that are receiving the input. What browser are you seeing this effect in? Have you tested in other browsers?
Is there a link where we can see the page (with the displaced area)?
(Still try the beta HTMLE, though - I haven't installed that yet).
Edit: What happens when you place the same text that was entered into the HTML Editor window directly into the content area of your web page?