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The obvious answer is performance. But I find that in order to make both the red notification icon at the top left and the blue notification icon on my responses tab go away, I have to click around to the item that caused the notification twice (accessing once from each method). Even if I am on the item and hit refresh. The result is that I am constantly wondering whether the notification I'm seeing is a new one or one I've already seen.

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Your experience isn't entirely as it seems (or at least shouldn't be). As soon as you open the StackExchange™ MultiCollider SuperDropdown™ or view the responses tab, the notification icon on each respective control should disappear regardless of whether or not you actually go to the relevant notification item (although in the former case, some people wished things worked a bit differently).

As for why you have to clear them independently and deliberately, I'll refer you to this answer by Kevin Montrose:

The responses tab and inbox show slightly different data.

The inbox doesn't include revisions, and the responses tab only shows activity on the current site. Viewing either clearing the unread count on the other would be incorrect.

...as well as this one.

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No, this is not quite what I was seeing before. Often the scenario I had is this (on SO): (1) I see a red 1 on my MultiCollider SuperDropDown. (2) I click the dropdown and click on the question title. (3) I'm on that page, and then click on my username. The red (1) is still there unless I hit Ctrl+Refresh. Perhaps this is a user agent-specific symptom, but now when I click on the dropdown, the red icon disappears immediately (before I even visit the question where the new comment appeared). <baffled> –  Aaron Bertrand Aug 19 '11 at 21:02
    
Ah I see. Well, it certainly wasn't supposed to behave like that. I'm not sure what would have caused that to happen. –  Tim Stone Aug 19 '11 at 21:43
    
It also behaves that way if I go to the item with the notification and then click back. But I understand why that functionality behaves that way and that it is mostly the browser driving it. –  Aaron Bertrand Aug 19 '11 at 21:48

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