Drupal adds unneeded folder to urls
Like i noted above, drupal thinks it's installed in a sub-folder because of the php-docroot lies in the parent-folder of the drupal-install, so it added /domain2/ to the $base_url.

To fix it, just edit your current settings.php in sites/* folder:

$base_url = 'http://domain2.tld';  // NO trailing slash!

Make sure settings.php is writable, it's often read-only!
(this was the problem here, otherwise i would've saved a lot of time searching a alternative ways to fix the $base_url... looks like there's a overhaul needed in my svn:post_commit-ftp_upload-script ;)