This actually fixed nothing. Unfortunately you didn't read the text in our download page, or the release notes (which were available for you to read in Live Update, before upgrading) before upgrading Akeeba Backup. As clearly noted, Akeeba Backup 3.9.X is not compatible with the old, vulnerable and obsolete Joomla! versions 3.0 OR 3.1 Furthermore, support for all previous versions of Akeeba Backup and Joomla! has ceased, effective November 20th 2013, 14:30 EET.
You can downgrade to Akeeba Backup 3.8.2 (not recommended) or upgrade your site to Joomla! 3.2 (very strongly recommended).
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!