Site question

I'm not sure if this is the place to ask about this or not, but it seems that any time I reply to comment on others' stories or my own, it starts a new comment branch rather than nesting under the comment that it's a reply to. This is despite the fact that I'm definitely clicking the "reply" link under the comments rather than typing directly into the comment box.

Is there something I can do or stop doing to make the replies nest? And are other users still notified that there's been a new comment made if the system doesn't mark it as a direct reply to their comment?