I have just encountered the problem upgrading to 3.6.2 in the Joomla update manager. (php 5.2, Joomla 2.5.6).
Akeeba stopped working with the following in the error_log.
PHP Fatal error: Class 'AEFactory' not found in /var/www/vhosts/boldhearts.com.au/httpdocs/administrator/components/com_akeeba/controllers/cpanel.php
Only when I downloaded and installed Akeeba Pro 3.6.2 did I get the message that I needed to upgrade to PHP 5.3. It looks like it is working ok now.
I am still very happy with your product.
regards
Justin Wright
traces of nut pty ltd