There are only a few significant differences between the default Ubuntu config and yours. First, it includes all of its <directory> containers inside the virtual host container. Secondly, it uses these Options:
Options Indexes FollowSymLinks MultiViews
and an allow from all directive inside the diectory containers:
<Directory /usr/www/>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
</Directory>
It wouldn't hurt to simply copy the default and add your specifics to it for each domain.
Also, you didn't mention (1) whether you are using rewrite rules and/or nice urls and (2) whether you've cleaned out the cache, i.e. using
delete. Although the instructions for DW say to use touch and purge, there's noting as rereshing as cleaning out the cache since some things just seem to hang around.
You must also restart apache every time you make changes to the configuration:
service apache2 restart