htaccess the same with and without permalinks

In a multisite install, htaccess remains the same when I set permalinks to default and when I set them to postname.

However the site links do change and work correctly, except for the search results url, that gets no permalink even if permalinks are set to postname. (I have opened a separate thread for this.)

My htaccess permissions are 656 (shared hosting, Godaddy, never changed them after the install).

The site htaccess:

# 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>

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).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]

# END WordPress