Comment 1 for bug 758976

The solution for this requires some thought. I recently had implemented functionality to do what is suggested - remove notifications after AJAX actions - and this had unintended bad consequences. See bug 754058.

One possible solution - tag each AJAX request with a header item which is sent back with the response, indicating that notifications are to be reset. That way AJAX requests in general (ie non user initiated ones which are done as part of a page load) will not reset the notifications but ones we choose to will.