If you get an alert for a thread you're tracking, and you view that thread from the link in your 'New Comments' area rather than using the alert it will still show. You can remove the alert by clicking 'ignore' on the alert. It should then clear.
If its not, please try clearing your browser cookies using the link below
You'll see a large white page with the text in the corner saying 'chess.com cookies cleared'. Once you see that, close the browser then re-open it and log back in
http://www.chess.com/clear_cookies.html

Hey , why my alert did not dissapear although I already see my alerts !! How to fix this problem ? The previous one do not dissapear and it kinda annoy me but the new one , im ok