Linux – Nginx welcome page returns

I'm running Nginx on an EC2 instance. I have a webpage installed in the default /usr/share/nginx/html dir. I've noticed that, if I make an AMI of that EC2 instance and a new EC2 instance using that AMI, the default Nginx welcome site (i.e index.html, 404.html, etc.) gets restored and overwrites my existing website where the files are the same. I can tell this by doing a git status in that dir and see that they've been added.

This is a bit of a pain because I'm running a SaaS product on the EC2 instance, and having customers see the Nginx welcome page looks a bit unprofessional.

My question is: what could be causing this?

Here is my nginx.conf:

# For more information on configuration, see:
#   * Official English Documentation: http://nginx.org/en/docs/
#   * Official Russian Documentation: http://nginx.org/ru/docs/

user  nginx;
worker_processes  1;

error_log  /var/log/nginx/error.log;
#error_log  /var/log/nginx/error.log  notice;
#error_log  /var/log/nginx/error.log  info;

pid        /var/run/nginx.pid;


events {
    worker_connections  1024;
}


http {
    include       /etc/nginx/mime.types;
    default_type  application/octet-stream;

    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
                      '$status $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    access_log  /var/log/nginx/access.log  main;

    sendfile        on;
    #tcp_nopush     on;

    #keepalive_timeout  0;
    keepalive_timeout  65;

    #gzip  on;

    # Load modular configuration files from the /etc/nginx/conf.d directory.
    # See http://nginx.org/en/docs/ngx_core_module.html#include
    # for more information.
    include /etc/nginx/conf.d/*.conf;

    #server {
    #    listen       80;
    #    server_name  *.xxx.com;
    #    return       301 https://$host$request_uri;
    #}

    server {
        listen        80;
        listen        443 default ssl;
        server_name  *.xxx.com;

        if ($http_x_forwarded_proto = "http") {
            return 301 https://$host$request_uri;
        }

        ssl_certificate /etc/pki/tls/certs/process.st.crt;
        ssl_certificate_key /etc/pki/tls/private/process.st.key;
        ssl_protocols SSLv3 TLSv1;
        ssl_ciphers ALL:!aNULL:!ADH:!eNULL:!LOW:!EXP:RC4+RSA:+HIGH:+MEDIUM;

        #charset koi8-r;

        #access_log  /var/log/nginx/host.access.log  main;

        location / {
            root   /usr/share/nginx/html;
            index  index.html index.htm;

            # Disable cache (for now).
            add_header Cache-Control no-cache;
        }

        # redirect server error pages to the static page /40x.html
        #
        error_page  404              /404.html;
        location = /40x.html {
            root   /usr/share/nginx/html;
        }

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

        # proxy the PHP scripts to Apache listening on 127.0.0.1:80
        #
        #location ~ \.php$ {
        #    proxy_pass   http://127.0.0.1;
        #}

        # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
        #
        #location ~ \.php$ {
        #    root           html;
        #    fastcgi_pass   127.0.0.1:9000;
        #    fastcgi_index  index.php;
        #    fastcgi_param  SCRIPT_FILENAME  /scripts$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;
        #}
    }


    # another virtual host using mix of IP-, name-, and port-based configuration
    #
    #server {
    #    listen       8000;
    #    listen       somename:8080;
    #    server_name  somename  alias  another.alias;

    #    location / {
    #        root   html;
    #        index  index.html index.htm;
    #    }
    #}


    # HTTPS server
    #
    #server {
    #    listen       443;
    #    server_name  localhost;

    #    ssl                  on;
    #    ssl_certificate      cert.pem;
    #    ssl_certificate_key  cert.key;

    #    ssl_session_timeout  5m;

    #    ssl_protocols  SSLv2 SSLv3 TLSv1;
    #    ssl_ciphers  HIGH:!aNULL:!MD5;
    #    ssl_prefer_server_ciphers   on;

    #    location / {
    #        root   html;
    #        index  index.html index.htm;
    #    }
    #}

}

Steps I did to create the base AMI image.

1. AWS EC2 Console: Launch Instance with Amazon Linux 64-Bit.
2. SSH into instance: sudo yum install git, sudo yum install nginx.
3. Edit the /etc/nginx/nginx.conf to the above.
4. Copy over all required SSL certs.
5. Delete default page at /usr/share/nginx/html.
6. Clone the Git repo to /usr/share/nginx/html.

Now I create the image:

1. ec2-create-image $INSTANCE_ID --name base.
2. AWS EC2 Console: Launch Instance using "base" AMI.
3. When it boots, it has the welcome page again along with the page I pulled from git, but the Nginx pages have overwritten the files that have the same name.