Mozdev.org is currently evaluating using Drupal for serving portions of its and its supported projects' websites. Specifically, we're looking to add blogging, wikis, and forums immediately, then also work to migrate other content into the system.

Mozdev currently services its projects as subdomains (www.mozdev.org, project1.mozdev.org, project2.mozdev.org, etc). Since we're looking to only add certain functionality to each site right now we'd like to just enable Drupal at certain urls for each site, for example:
www.mozdev.org/blog
www.mozdev.org/forum
www.mozdev.org/wiki
www.mozdev.org/admin

project1.mozdev.org/blog
...

I have multi-site setup and working with clean urls for multiple sites by adding the other projects to the sites/ directory (this may be done from only inside the default site by setting the prefixes through scripting later), but I'm having problems pulling Drupal into an existing site using aliases while leaving the clean urls enabled.

My Apache virtualhost:

<VirtualHost *:80>
    ServerName locdrupal
    ServerAlias locdrupal locdrupal1 locdrupal2

    DocumentRoot "/home/silfreed/src/mozdev/drupal/fakeroot"

    <Directory "/home/silfreed/src/mozdev/drupal/fakeroot">
        Options Indexes FollowSymLinks
        AllowOverride None
        Order allow,deny
        Allow from all
    </Directory>

    Alias /blog /home/silfreed/src/mozdev/drupal/drupal
    Alias /forum /home/silfreed/src/mozdev/drupal/drupal
    Alias /wiki /home/silfreed/src/mozdev/drupal/drupal
    Alias /admin /home/silfreed/src/mozdev/drupal/drupal
    <Directory "/home/silfreed/src/mozdev/drupal/drupal">
        RewriteEngine on
        RewriteBase /
        RewriteCond %{REQUEST_FILENAME} !-f
        RewriteCond %{REQUEST_FILENAME} !-d
        RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]

        Options Indexes FollowSymLinks
        AllowOverride None
        Order allow,deny
        Allow from all
    </Directory>
</VirtualHost>

When I view http://locdrupal I get the "fakeroot" content just fine - when I goto http://locdrupal/blog I get Drupal, but it thinks it's at the main level (ie, not inside the "blog" menu item). So this breaks for the other menus as well.

Any ideas what could be going on here?

-Doug