Can't access new WP install on subdirectory

Question

I'm having this issue: I have a WP install on root. So far so good.

Now I'm installing another version on a subdirectory, and it doesn't work. I have done this many times before, but maybe because of a server configuration, maybe something changed on new WP versions, it doesn't work in this case. It doesn't create permalinks (I have checked permissions) and if I use a custom structure, it goes to the main install and displays its 404 page. However, if I set permalinks as plain, it displays just fine.

Another thing I noticed is that if I try to customize the site, it asks me to log in because my session has finished. No matter how many times I try to log in, it kicks me out.

Just in case, WordPress Address (URL) and Site Address (URL) are correct, with no trailing slash, but they look grayed out. I also added the following lines to wp_config.php to no avail

define('WP_HOME','https://www.example.com/landing');  // NO trailing slash at the end
define('WP_SITEURL','https://www.example.com/landing'); // NO trailing slash at the end

Anyways, I spent the last hours checking documentation and similar questions here and on other sources, but nothing works and I'm completely lost. Any idea on what am I doing wrong, or what can I do to force this to work?

EDIT

I see that the wp-config file on root has this code added, don't know if it matters, but adding it just in case (IP address edited):

if( ini_get("max_input_vars") < 5000)
{
    echo "Set max_input_vars upto 5000";
    exit;
}

if($_SERVER['REMOTE_ADDR'] == '123.123.123.123')
{
    define('DISALLOW_FILE_MODS',false);
}
else
{ 
    define('DISALLOW_FILE_MODS',false);
}

and .htaccess file on root:

#<FilesMatch ".(eot|ttf|otf|woff|css|js|svg)">
#    Header set Access-Control-Allow-Origin "*"
#    </FilesMatch>
Header set Access-Control-Allow-Origin "https://beta.example.com"
# Block WordPress xmlrpc.php requests
<Files xmlrpc.php>
order deny,allow
deny from all
allow from 111.111.111.33
allow from 206.111.111.184
allow from 206.111.111.185
allow from 127.0.0.1
</Files>
RewriteCond %{REQUEST_METHOD} ^(TRACE|TRACK)
RewriteRule .* - [F]

php_value max_input_vars 5000 

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress


<IfModule mod_headers.c>
    ExpiresActive On
    ExpiresDefault A29030400
    <FilesMatch "\.(jpg|jpeg|gif|png|js|css)$">
      ExpiresDefault A7200 
      Header append Cache-Control "private, must-revalidate"
    </FilesMatch>
</IfModule>

AddOutputFilterByType DEFLATE text/plain
#AddOutputFilterByType DEFLATE text/html
AddOutputFilterByType DEFLATE text/xml
AddOutputFilterByType DEFLATE text/css
AddOutputFilterByType DEFLATE application/xml
AddOutputFilterByType DEFLATE application/xhtml+xml
AddOutputFilterByType DEFLATE application/rss+xml
AddOutputFilterByType DEFLATE application/javascript
AddOutputFilterByType DEFLATE application/x-javascript

<Files *.htm>
    #Compress
    SetOutputFilter DEFLATE
</Files>

# start Emerson adds

# Protect wp-config.php file
<files wp-config.php>
order allow,deny
deny from all
</files>

# Block the include-only files
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^wp-admin/includes/ - [F,L]
RewriteRule !^wp-includes/ - [S=3]
RewriteRule ^wp-includes/[^/]+.php$ - [F,L]
RewriteRule ^wp-includes/js/tinymce/langs/.+.php - [F,L]
RewriteRule ^wp-includes/theme-compat/ - [F,L]
</IfModule>

# Prevent people from browsing the content of your directories
Options All -Indexes

# Protect the .htaccess file itself
<Files .htaccess>
order allow,deny
deny from all
</Files>

# block ip addresses from login to the site
# order allow,deny
# deny from 456.123.8.9
# allow from all

## EXPIRES CACHING ##
<IfModule mod_expires.c>
ExpiresActive On
ExpiresByType image/jpg "access 1 year"
ExpiresByType image/jpeg "access 1 year"
ExpiresByType image/gif "access 1 year"
ExpiresByType image/png "access 1 year"
ExpiresByType text/css "access 1 month"
ExpiresByType application/pdf "access 1 month"
ExpiresByType text/x-javascript "access 1 month"
ExpiresByType application/x-shockwave-flash "access 1 month"
ExpiresByType image/x-icon "access 1 year"
ExpiresDefault "access 2 days"
</IfModule> 
## EXPIRES CACHING ##

Answer 1

From your comment I know that you are using nginx. Nginx need a bit different configuration than Apache. Probably your current nginx vhost looks like that.

server {
  listen *:80;
  server_name           test.dev;
  root                  /var/www/test;

  access_log            /var/log/nginx/access.log;
  error_log             /var/log/nginx/error.log;

  index index.php index.html;

  location / {
    # try to serve file directly, fallback to index.php
    try_files $uri $uri/ /index.php?$args;
  }

  location ~ \.php$ {

    include fastcgi.conf;

    fastcgi_pass 127.0.0.1:9070;
  }
}

The key part of this configuration is:

location / {
  # try to serve file directly, fallback to index.php
  try_files $uri $uri/ /index.php?$args;
}

it tell us something like that:

For location beginning with / character try to load file from file system and if there is no such a file rewrite to index.php with arguments.

So thats why when you are trying to visit your subdir site it is working for something like /subdir/index.php?p=100 because file /subdir/index.php is existing so there is no need for redirection. However when you try to visit /subdir/lorem-ipsum/ you will be redirect to home because there is no /subdir/lorem-ipsum/ file.

Correct configuration for both root and subdir WordPress installation will be:

server {
  listen *:80;
  server_name           test.dev;
  root                  /var/www/test;

  access_log            /var/log/nginx/access.log;
  error_log             /var/log/nginx/error.log;

  index index.php index.html;

  location / {
    # try to serve file directly, fallback to index.php
    try_files $uri $uri/ /index.php?$args;
  }

  location /subdir {
     # try to serve file directly, fallback to index.php
     try_files $uri $uri/ /subdir/index.php?$args;
  }

  location ~ \.php$ {

    include fastcgi.conf;

    fastcgi_pass 127.0.0.1:9070;
  }
}

PS. Nginx doesn't care about .htaccess you can remove it.