I've got the same setup as you. Are they wrong or just not showing? Console errors?
Also, not sure if this is by design, but after I post an in-place reply, I have to reload the page to see my post. However, upon editing a post, the page reloads immediately. I didn't see any error in the console.
As for the other problem, I'm confused about why that's the only thing not working. Are you running any other extensions that could be conflicting?
EDIT: I have no idea why, but as I was hammer-clicking on the Hacker News main button, all of a sudden the unread counts started to appear. I wonder if there was some cache issue or something such as that.