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I suspect the add ons and fork mentioned are not relevant. I see a persistent notification circle on standard Firefox with no add ons. It doesn't seem to be completely consistent but the general behaviour I see is as follows:

- I see a blue circle indicating I have a notification.
- I open the notifications panel and click on the notification.
- The relevant page opens, showing the answer or comment the notification referred to.
- The blue circle is still present at the top of the page and the notification is still marked as unread.
- If I open the notifications panel while already on this destination page, clicking on the notification takes me to the answer or comment (which does not involve changing to a different page) and the blue circle disappears and the notification is marked as read.

Note that this behaviour when already on the destination page seems to depend on it being the exact destination (so the URL of the answer to a question if the notification referred to that answer - the URL of the question is not sufficient). This makes me wonder if it is the lack of requirement for a page load that allows the functionality to work, and a page load suppresses it, causing the mark as unread to fail.