I'm Linux newbie so you may have to bear with me a little here.
Using a 3rd party KVM-based VM I created a nginx + MySQL + PHP server from an ISO of the core-11.3-lucid-x86 appliance and then used an unmodified TKLBAM configuration to back it up via the Hub to S3. A default server, half a dozen WordPress sites and phpMyAdmin were all working perfectly before the backup.
I then used the "Restore this backup to a new cloud server" facility in the Backups dashboard to create a new micro instance on EC2.
In exploring the new instance I noticed that the links in "/usr/local/nginx/sites-enabled" were restored as files and "config-db.php" and "htpasswd.setup" in "/etc/phpmyadmin" were restored with incorrect permissions (Group set to root instead of www-data) causing phpMyAdmin not to work correctly. Also a previously deleted "/var/www/index.html" was present in the restore.
After reading the TKLBAM documentation and FAQ I can also see that the file "hbr" and the folder "profile" are missing from "/var/lib/tklbam" in the new instance but presumably this could be because I haven't yet performed a backup from this new instance? (They existed in the original and I didn't modify them at all.)
Coming from a Windows background where I have lots of experience of backing up and restoring using drive imaging software I find these differences in source and destination a little unnerving.
What is it I need to know in order to use the "Restore this backup to a new cloud server" facility and end up with an exact clone of the original?