There is a bug in the current thematic base theme.
Simplified markup for comments:
div#comment-list
ol
li.comment
li.comment
ul.children
li.comment
If one of the above li.comment has an ol or ul in them, then it is styled (incorrectly) as a comment list, not as a normal entry list.
A partial work around is to change the "#comment-list li" rules to "#comment-list li.comment" and to change "#comment-list ul" to "#comment-list ul.children". However, there isn't any fix for "#comment-list ol" because it doesn't have a class on it.
Ciao!