If you encounter,
Could not back up sites directory for drupal
when trying to back up a site using Aegir, then this is because there are some permission issues with some of the files in the sites directory.
In my case, these files were in the private/temp/ directory. Listing all offending files can be done by the following command:
find . | grep private/temp/
If anything other than the usual .htaccess file is found, then that is probably a likely culprit. Checking file permissions should confirm this.