Nginx frequently returns 404 PHP FPM

I have a server with Nginx 1.4 in Ubuntu 14.04 and it’s running with PHP5-fpm. The server has multiple domains and sub-domains in a Private cloud server. The server is getting consistent hits from traffic and it’s lot. Everything is fine, but Nginx frequently returns 404, while the case is not in actual and after couple of try it returns the actual output instead of 404. Below is one example of my one of the server block from nginx config.

server {
    listen 80;
    #listen [::]:80;

    root /var/www/appfolder;
    index index.php index.html index.htm;

    # Make site accessible from http://localhost/
    server_name domain-name;

    location / {
        # First attempt to serve request as file, then
        # as directory, then fall back to displaying a 404.
        try_files $uri $uri/ =404;
        # Uncomment to enable naxsi on this location
        # include /etc/nginx/naxsi.rules
    }

    # Only for nginx-naxsi used with nginx-naxsi-ui : process denied requests
    #location /RequestDenied {
    #   proxy_pass http://127.0.0.1:8080;    
    #}

    error_page 404 /404.html;

    # redirect server error pages to the static page /50x.html
    #
    error_page 500 502 503 504 /50x.html;
    location = /50x.html {
        root /var/www/appfolder;
    }

    # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
    #
    location ~ \.php$ {
        try_files $uri =404;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
    #   # NOTE: You should have "cgi.fix_pathinfo = 0;" in php.ini
    #
    #   # With php5-cgi alone:
    #   fastcgi_pass 127.0.0.1:9000;
    #   # With php5-fpm:
        fastcgi_pass unix:/var/run/php5-fpm.sock;
        fastcgi_index index.php;
                fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
        include fastcgi_params;
    }

    # deny access to .htaccess files, if Apache's document root
    # concurs with nginx's one
    #
    #location ~ /\.ht {
    #   deny all;
    #}
   }

Please help me on this, I have searched a lot, but never got a proper solution. Thanks in advance.