Sorry – didn’t read the first paragraph (too late/early).
Did you try several in a row to see if it had any effect at all?
If there was no effect then I would guess that it’s a CSS issue.
Do you still know what the original trackback code was?(Any CSS involved?) It might give a clue as to what’s missing.
looks like you just need a line break.
search for [ol id=”commentlist”] and add a [br /] (replace [ ] with < > ) above it. In the comments file I think.
Just FYI but in firefox the menu on the left disappears to the bottom of the page (didn’t check IE).