multisite not good for SEO

I’m running a network of mutltisites using subdirectories.
The network is an online magazine.
Each site represents an issue of the magazine, with the parent site being an “about us” site.

I’ve been checking the SEO of each issue using a number of online SEO analysers.

I’ve found that the top level site is fine, but the sub-sites (issues) do not score well. The problem seems to be that the SEO analysers don’t see the content, for example they report that there is no HEAD section, no TITLE tag in the header, no H1 on the page, etc etc.

When I view the page source I can see they are there.

The analysers report the header as 301.

I’m not an expert on .htaccess files, but I’m guessing that the re-direct is how WP handles the sub-sites and redirects visitors to the sub-site.

My .htaccess is given below.

Can anyone explain what is happening here, and how I can overcome it?
TIA,
Rob

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [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).*) $1 [L]
RewriteRule ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
RewriteRule . index.php [L]
<Files 403.shtml>
order allow,deny
allow from all
</Files>`