Serve sub-directory inside a root as another sub-domain with SSL

Question

I have a working NGINX configuration for multiple sub-domains. I have enabled SSL for them by using a Let's Encrypt/ACME client. All of the sub-domains are working except one.

One of the sub-domain is served under /var/www/dir as https://dir.domain.net and another one is served under /var/www/dir/one as https://one.domain.net. For some reason I can not understand, the sub-domain served under /var/www/dir/one is being redirected to https://dir.domain.net after enabling SSL.

Configurations for this two sub-domains as follow:

/var/www/dir as http://dir.domain.net

server {

listen 80;
listen 443 ssl spdy;
root /var/www/dir;
index index.php index.html index.htm;
server_name dir.domain.net;

add_header Strict-Transport-Security max-age=31536000;
add_header X-Frame-Options SAMEORIGIN;
ssl on;
ssl_certificate cert.crt;
ssl_certificate_key key.pem;
ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
ssl_session_cache shared:SSL:10m;
ssl_session_timeout 5m;
ssl_stapling on;
ssl_stapling_verify on;
ssl_trusted_certificate trustedCA.pem;
resolver 8.8.4.4 8.8.8.8 valid=1800s;
resolver_timeout 10s;
ssl_dhparam dhparam.pem;
ssl_prefer_server_ciphers on;
ssl_ciphers EECDH+ECDSA+AESGCM:EECDH+aRSA+AESGCM:EECDH+ECDSA+SHA384:EECDH+ECDSA+SHA256:EECDH+aRSA+SHA384:EECDH+aRSA+SHA256:EECDH:EDH+aRSA:!RC4:!aNULL:!eNULL:!LOW:!3DES:!MD5:!EXP:!PSK:!SRP:!DSS;

if ($scheme = http) {
    return 301 https://$server_name$request_uri;
}

location / {
    try_files $uri $uri/ /index.html =404;
    rewrite /index.php/(topic|board),(.*).html$ /index.php?$1=$2 permanent;
    rewrite /index.php/(topic|board),(.*)$ /index.php?$1=$2 permanent;
    rewrite /index.php(\?|%3F)(topic|board)(=|%3D)(.*)$ /index.php?$2=$4 permanent;
    rewrite /subdomains/dir/index.php/(topic|board),(.*)$ /index.php?$1=$2 permanent;
    }


    location ~ \.php$ {
    fastcgi_pass unix:/var/run/php5-fpm.sock;
    fastcgi_index index.php;
    fastcgi_read_timeout 90;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
    fastcgi_param SSL_PROTOCOL  $ssl_protocol;
    fastcgi_param SSL_CIPHER    $ssl_cipher;
    fastcgi_param SSL_SESSION_ID    $ssl_session_id;
    fastcgi_param SSL_CLIENT_VERIFY $ssl_client_verify;
    include fastcgi_params;
     }
 }

/var/www/dir/one as https://one.domain.net:

server {
root /var/www/dir/one;
index index.php index.html index.htm;
server_name one.domain.net;

# log directives

add_header Strict-Transport-Security max-age=31536000;
add_header X-Frame-Options SAMEORIGIN;
ssl on;
ssl_certificate cert.crt;
    ssl_certificate_key key.pem;
    ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
    ssl_session_cache shared:SSL:10m;
    ssl_session_timeout 5m;
    ssl_stapling on;
    ssl_stapling_verify on;
    ssl_trusted_certificate trustedCA.pem;
    resolver 8.8.4.4 8.8.8.8 valid=1800s;
    resolver_timeout 10s;
    ssl_dhparam dhparam.pem;
    ssl_prefer_server_ciphers on;
    ssl_ciphers EECDH+ECDSA+AESGCM:EECDH+aRSA+AESGCM:EECDH+ECDSA+SHA384:EECDH+ECDSA+SHA256:EECDH+aRSA+SHA384:EECDH+aRSA+SHA256:EECDH:EDH+aRSA:!RC4:!aNULL:!eNULL:!LOW:!3DES:!MD5:!EXP:!PSK:!SRP:!DSS;                                                                                           

location / {
    try_files $uri $uri/ /index.html;
    rewrite /index.php/(.*)$ /index.php?title=$1 permanent;
}

location ~ \.php$ {
    #fastcgi_pass unix:/var/run/php5-fpm.sock;
    fastcgi_pass phpservers;
    fastcgi_index index.php;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
    include fastcgi_params;
}
}

In order to serve /var/www/dir/one as https://one.domain.net, what should I do?

Thanks in advance.