So, when I put in my .htaccess file which contains the following:
# Use PHP5 php.ini as default
AddHandler application/x-httpd-php5 .php
AcceptPathInfo On
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php/$0 [L,QSA]
The server tries to download the PHP file instead of executing it. When I remove the .htaccess file, everything works fine and the PHP files execute.