mod_alias site directories does not work

Apache 2.2.3
php 5.2.0

I have a multi site setup where all sites use the drupal root setup as DocumentRoot, and sites/ in another directory.

Each site will have it's own VirtualHost section in apache conf

In each VirtualHost section there is an alias for sites/all and one for sites/thatsite

I can see that the alias statements are working, because if I go to a URL such sites/thatsite/themes/themename/logo.png, I can see the logo
Also If I go to sites/thatsite/settings.php I get a blank page rather than an error

Drupal obviously isn't seeing the same thing as me as it wants to install a new site in sites/default

Example VirtualHost settings:

ServerName cathywheeler.com
ServerAdmin admin@cathywheeler.com
ServerAlias www.cathywheeler.com

DocumentRoot /srv/squeed01/drupal/drupal6/

Options FollowSymLinks
AllowOverride All

ErrorLog /var/log/apache2/error.log

# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
LogLevel warn

CustomLog /var/log/apache2/access.log combined
ServerSignature On

# Various rewrite rules.

RewriteEngine on
# If your site can be accessed both with and without the 'www.' prefix, you
# can use one of the following settings to redirect users to your preferred
# URL, either WITH or WITHOUT the 'www.' prefix. Choose ONLY one option:
#
# To redirect all users to access the site WITH the 'www.' prefix,
# (http://example.com/... will be redirected to http://www.example.com/...)
# adapt and uncomment the following:
RewriteCond %{HTTP_HOST} ^cathywheeler\.com$ [NC]
RewriteRule ^(.*)$ http://www.cathywheeler.com/$1 [L,R=301]
#
# To redirect all users to access the site WITHOUT the 'www.' prefix,
# (http://www.example.com/... will be redirected to http://example.com/...)
# uncomment and adapt the following:
# RewriteCond %{HTTP_HOST} ^www\.example\.com$ [NC]
# RewriteRule ^(.*)$ http://example.com/$1 [L,R=301]

# Modify the RewriteBase if you are using Drupal in a subdirectory or in a
# VirtualDocumentRoot and the rewrite rules are not working properly.
# For example if your site is at http://example.com/drupal uncomment and
# modify the following line:
# RewriteBase /drupal
#
# If your site is running in a VirtualDocumentRoot at http://example.com/,

# uncomment the following line:
# RewriteBase /

Alias /sites/cathywheeler.com /srv/squeed01/drupal/sites6/cathywheeler.com

Options FollowSymLinks
AllowOverride All