Hi Kevin, great plugin! I have searched back through a few forum posts involving the file filter and currently experiencing some of the same issues. I have a fresh install of WP 3.0.1, RS 1.2.8 beta2, Twenty Ten theme, activated File Filter, uploaded a file and inserted it onto the About page. 

I ran Attachment Utility and it detected the file located on the "About" page correctly, however the file is still accessible via direct URL and via directory index of/wp-content/uploads.

I am using a sub-domain, would this cause any issues?  

The subdomain root .htaccess file has the following..

# 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>

# END WordPress

 There is no .htaccess under wp-content/uploads (saw a mention of this in another forum post)

Am I missing a step? Thanks for any advice. I can give you admin access if that would help resolve. 

Thanks, Matt