How curious. What’s in your .htaccess?
I’m experiencing a similar problem. see here http://wordpress.org/support/topic/122042?replies=1
This is my .htaccess file under the blog/ directory in my site root:
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /blog/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /blog/index.php [L]
</IfModule>
# END WordPress
I have WP installed under blog/ directory in my site root.
The pages under blog/ and / actually don’t return 404 code. Instead all pages that are under different directories return 404 code:
/var/www/site/ (200/OK)
/var/www/site/blog/ (200/OK)
/var/www/site/anyotherdir (404/ERROR) – not indexed by search engines but still able to see on browser
If I disable pretty permalinks the problem goes away.
hel apreciated.