Hm, yeah, the "Reply" button doesn't link to "#comments" the way the "X Comments" link does, so if you just go directly to "Reply" from the reading page, it opens the actual reply page (the "mode=reply") instead of opening the comments page and popping open the javascript reply box.

I never really noticed being at the top of the entry, but it does always annoy me that if I click the reply link, it won't show me comments that already exist.