When I enable modules on the CiviCRM codebase either loaded by Octopus or by a new platform, Aegir Barracuda looses the configuration file for CiviCRM.
Octopus 2.0.8 & 2.0.9 (tried both) with Barracuda 2.0.8 & 2.0.9
Install CiviCRM platform, login, go to modules and enable several modules (really does not matter which ones). After Drupal processes modules and enables them, it can not find the civicrm.settings.php file and says that CiviCRM is not installed and to install it. Sometimes if you click on the link to install it it will say that CiviCRM is already installed, sometimes it will install it again but it will not function correctly. When a reinstall occurs, the civicrm.settings.php file is put into the 'default' folder instead of the website's folder under sites/mywebsite.com
I have setup 3 platforms separately and used the Octopus build as well. None of them work correctly and all have the same error.
One more thing, I was having problems on one server at Amazon so I setup a fresh Linode and I am still having the same issue