Updating duplicate Flags AND one or more Views blocks on a page on Flag click
I just ran into the same problem. This is how I handled updating duplicate flags on a page:

    $(document).bind('flagGlobalAfterLinkUpdate', function(event, data) { 

        if(data.flagStatus == "unflagged"){
            $('.flag-favourite-' + data.contentId + ' a').each(function(){
                if(!$(this).find('a').hasClass('unflagged')){ 
                        ($(this).html(data.link.innerHTML));                            
               }
            });                
        }
        else{

            $('.flag-favourite-' + data.contentId).each(function(){                  
                if(!$(this).find('a').hasClass('flagged')){ 
                        ($(this).html(data.link.innerHTML));                            
               }
            });               

        }
    });


change out the term favourite with the machine name of you flag and it should work...