I recently upgraded to 2.8.6 and have some strange issues.
My main blog, http://www.domain.com/blogs/ loads fine.
As does the admin panel at http://www.domain.com/blogs/wp-admin
My other blogs, do not seem to work properly.
If someone visits http://www.domain.com/blogs/blogname they get a 404 not found, but when I visit http://www.domain.com/blogs/blogname/wp-admin I get brought to the login screen.
The next weird thing is, I cannot login to my sub-blogs. I get told "You do not have permission to access this blog".
When I check my main wp-admin control panel it shows that the user I am trying to login with is an admin on the secondary blog.
If I create a new blog, the same thing happens..
My .htaccess file is below
RewriteEngine On
RewriteBase /blogs/
#uploaded files
RewriteRule ^(.*/)?files/$ index.php [L]
RewriteCond %{REQUEST_URI} !.*wp-content/plugins.*
RewriteRule ^(.*/)?files/(.*) wp-content/blogs.php?file=$2 [L]
# add a trailing slash to /wp-admin
RewriteCond %{REQUEST_URI} ^.*/wp-admin$
RewriteRule ^(.+)$ $1/ [R=301,L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule . - [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-.*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]