I am no longer receiving notifications or emails when someone replies to my comments. This makes it difficult to keep a conversation going. For instance, I commented here (and received an email about the necromancer achievement), but have not received notifications or emails when Kenneth replies. All check boxes are checked under Settings > Notifications. My spam folder is empty.
While I have your attention, I'd like to mention that the "reply" button is (still) missing on recent comments in threads. See below:
If I right-click and inspect the web page, the reply buttons appear (this has been my main workflow for a while now, and it's getting old fast).