Directory structure problems

After upgrading to 2.0 I noticed my directory structure appears to be acting weird:

I tried accessing my /stats/ directory to check my monthly web server stats and now I keep getting my blog main page instead.

I checked my .htaccess file:

ErrorDocument 404 /404

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php
</IfModule>

# END WordPress

It’s smaller than it used to be in v1.5. I deleted the code between # BEGIN WordPress and # END WordPress, and was able to access my /stats/ directory again. But permalinks don’t work with that missing code. So I rebuilt my .htaccess file and now I can’t access the /stats/ directory again.

Also trying to access directories that don’t exist, eg: https://www.escape-key.com/nada/ , I still get the blog main page.

Any ideas?