I've been receiving minor warnings whenever I try and verify a site. If there's even a single file without the correct aegir:www-data permissions, you'll get a yellow warning when the site verifies. The most common one I see is:
Could not change permissions sites/mydomain.com to 493 (chmod to 755 failed on sites/mydomain.com)
If you're new to Aegir like me but want to get rid of the file permissions error, you can try these commands:
cd /var/aegir/platforms/drupal-6.16/sites
chown -R aegir:www-data mydomain.com/*I've got Aegir running at work and on my personal VPS and have had trouble with file permissions mainly due to the TinyMCE module. (All files are uploaded with www-data:www-data permissions.) By running the above commands and then doing a Verify, everything shows up green and clear.