There should be a "reply to this" link beneath each comment. If you're not seeing this, you've likely not got your account properly configured. Drop a line to Rusty (rusty@kuro5hin.org). I'd also send a screenshot, helps to identify what's what.

Might also be a delay on new accounts being able to post, though I haven't seen any data on this being implemented. Basically a way to slow down spammers and trolls, it's been discussed in the past.