Comment reply form not working? When I click 'reply' button on the comment, a new comment form open in new Windows; but subject box does not contain 're:' or like that and my reply saves as a new comment.

How can I repair my comment system?

Regards.
you need to go to admin/structure/types/manage/article [if your content type is Article] or admin/structure/types/manage/page [if it's Basic Page]

click on comment settings and make sure you have threading checked, so the replies have an indentation. 

Asfar as re: in subject box, to my knowledge, drupal does not come with that by default.