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For the past few weeks, the notification box on my MSE intray icon has been showing me as having 2 or 3 unread messages (see image below). I go to the posts and read the comments but that doesn't clear the notification box. Some messages add to theenter image description here total but get subtracted when I read them, but 3 are now persistent. Am I doing something wrong?

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As noted, this behavior changed several months ago. This is noted in this meta post.

I know two ways of clearing the flag:

  1. If you click on the actual "envelope" icon in the dropdown, you can flip an individual's notification's status between "read" and "unread".

  2. In the drop-down at the top, you can click on "Mark all as read", which will clear them all.

But, as you note, simply clicking on the notification to go to the corresponding comment/post may not clear the notification (unless your interface happens to interpret your click as having "hit" the envelop icon...)

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