WordPress multisite – Sub-directory not working in Admin

I just setup a fresh WordPress multisite using Sub-directories

It all seems fine, I can browse the Admin section and can see the live site (which has no pages, posts or comments at the moment…)

I then go in the Admin section to “Sites” > “All Sites” from the left hand navigation.

And when I click there on Sites “Add New” I get a broken link because the link is missing the main sub-directory (https://sub-domain.domain.com/wp-admin/network/site-new.php)

However, if I try to add a site from “Sites” > “Add New” from the left hand navigation it works (https://sub-domain.domain.com/sub-directory/wp-admin/network/site-new.php)

But it brakes again here once I press submit since the form seems to miss the sub-directory again (https://sub-domain.domain.com/wp-admin/network/site-new.php?action=add-site)

The same problem of the missing sub-directory in the root is also when I try to click on any link form the TOP admin Navigation:
“My Sites” > “Network Admin” > “Dashboard” or
“My Sites” > “Network Admin” > “Sites” or
“My Sites” > “Network Admin” > “Users” or
“My Sites” > “Network Admin” > “Themes” or
“My Sites” > “Network Admin” > “Plugins”

Any idea what is causing this inconsistency in regards of the sub-directory

I am using the same .htaccess in the sub-domain and in the sub-directory:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ – [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) subdomain/subdirectory/$2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ subdomain/subdirectory/$2 [L]
RewriteRule . index.php [L]
</IfModule>
# END WordPress