Please 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
You can downgrade to Akeeba Backup 3.8.2 (not recommended) or upgrade your site to Joomla! 3.2 (very strongly recommended). Joomla! 3.1 is end of life, this is why it is no longer supported. Our policy has always been that we only support the current LTS and STS version of Joomla! which, at the time of this writing, are 2.5 and 3.2 respectively.
As to your template provider, I am using a RocketTheme template on my development Joomla! 3.2 site since one month ago, when the Joomla! 3.2 alpha was released. I don't have any problems. Further to that: RocketTheme, just like all developers, had 2 months to test their software with Joomla! 3.2 as the release date was pushed back from September to November. Moreover Joomla! published an alpha, two betas and an RC of Joomla! 3.2. The changes between 3.1 and 3.2 are minimal, mostly having to do with the rewrite of JApplication to extend JApplicationWeb instead of being a bespoke mess of slapped together code. Changes to let the software conform to the new Joomla! version only take one or two days, while replying to support requests. Been there, done that, got the t-shirt. Granted, the enhanced JLayouts may be more challenging but JLayouts have been announced 9 months ago and the changes to Joomla! 3.2 views have been around for nearly 4 months. Where were they all that time?
At some point you, the users, have to exert pressure to extension developers –including template developers– to provide support for the upcoming Joomla! versions. I can't possibly be the only extensions developer who downloads the latest Joomla! branch from Git and test my software against it! Forward compatibility, when spread in the span of 6+ months, is dead easy and only takes roughly half hour every week. I know that because I do that. So, please, just voice your concerns to your component, module, plugin and template developers. Let them know that your business depends on Joomla! and you can't afford to run an obsolete, vulnerable version of the software because they don't bother doing their due diligence on time. It really boils down to that.
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!