It's nice that the "inbox" control now refreshes real-time instead of waiting for a new page load, and it's also nice that "inline" notifications of new questions/answers/comments are given on the page. However, the two notification methods don't seem to be talking to each other well.
Example: if I'm viewing a page on which I have an answer or comment posted, and a new comment to that answer comes in, I get both the inbox notice and the inline notice of the new comment. If I respond to the inline notice to load the new comment on the page, the inbox notification does not reset.
This is mildly annoying, as the inbox notification is no longer a reliable indicator that I have something new I haven't looked at.