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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.

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Responding to a comment has never marked your inbox as read, this isn't anything new (there may be other content, or multiple comments, or any number of things you may or may not have actually seen).

The inbox is only marked read by explicitly reading it directly.

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