I was about to edit my comment to mention that: HN delays showing the "reply" link on deeply nested comments. It's an ancient flame retardant. You can, however, get around it by clicking "link" on the comment you want to reply to.
You can always click the "link" button fer the specific comment and then you'll see a reply button -- it's nothing account-specific, it's just one weird trick to slow down flamefests proportionally to comment depth.
Thanks, that's exactly what it was! That's why the "reply" button was not appearing, and I thought I was rate-limited. This very thing happened to your comment - I am replying by visiting the permalink.