new site tries to download instead of loading

I am running WordPress 4.4.2 network and I have two sites configured for subdomains and running fine. I added a new site using the “new Site” tool on the network dashboard. When trying to access the new site index.php, wp-admin.php, wp-login.php, etc. it tries to download instead of loading the page.
Here is my .htaccess file

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
# add a trailing slash to /wp-admin
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^(.*\.php)$ $1 [L]
RewriteRule . index.php [L]
php_value upload_max_filesize 64M
php_value post_max_size 64M
php_value max_execution_time 200
php_value max_input_time 200

I am not running any caching plugins. I have wordfence installed, but I tried disabling that too and nothing has worked.

The plugins installed are:
add from server
are you a robot?
backWPup
Code Embed
Embed any Document
Enhanced Media Library
FAst Secure Contact Form
Hellow Dolly
Namaste LMS
TM Replace Howdy
Watu
Wordfence Security
WP RSS Aggregator
WPtouch mobile plugin
YouTube Embed WpDevArt.

I´ve tried deactivating all of them, to no effect.

The site is installed in the root html folder and I´ve checked all subdirectories and there is no other .htaccess file on the server.