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try this apache option

Hi Michael,
I'll just take a wild guess - if you are running on your local machine, maybe you are specifying your URL something like: http://localhost:3004 to specify one domain, http://localhost:3005 for the other domain, etc...  But apache might be telling drupal literally that the site is http://localhost:3004 - when you want it to say http://example.com - do you follow?  So drupal looks in /sites/localhost:3004/* for the files, instead of /sites/example.com/* - you need to get apache to change the URL to http://example.com before passing it to drupal.  Try adding something like this to your .htaccess file:

Listen 3004
Listen 3005
Listen 3006

<VirtualHost 127.0.0.1:3004>
ServerAdmin temp [at] temp [dot] com
DocumentRoot "c:/path/to/drupal/root"
ServerName example.com
</VirtualHost>

<VirtualHost 127.0.0.1:3005>
ServerAdmin temp [at] temp [dot] com
DocumentRoot "c:/path/to/drupal/root"
ServerName example-2.com
</VirtualHost>

<VirtualHost 127.0.0.1:3006>
ServerAdmin temp [at] temp [dot] com
DocumentRoot "c:/path/to/drupal/root"
ServerName example-2.com
</VirtualHost>

In one case I also had to specify the following directive inside the VirtualHost section for a particular site (I think that site was always going to the install screen, but I can't remember for sure) - you might also try it:
 
usecanonicalname on

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