I presume that if I click the QR link on a specific post then the QR box becomes a reply to that post

It does not. It just jumps to the QR entry fields at the end of the page, which always responds to the latest post.

Edit: Actually, it doesn't even seem to jump. It's a link to javascript:quickReply(#), which doesn't seem to do anything. If I'm basing my response above on a bug, either in the BBS software or my browser, I apologize. Actually, IE even reports an error when I click the QR link next to posts.