This potentially exciting state of affairs is half reported by a website that read another site's rambling on the subject (I respect Ars Technica, but their source is The Register). The Ars article confuses the European Union with the European Patent Office, two different things, ruled by different treaties and having different nations as members. And it's bizarre that The Reg's article is actually written by OUT-LAW.COM, who provide reasonably good reviews of Intellectual Property issues, so I'm puzzled how the normally-good Ars Technica got confounded.
But the best source in my book is the IPKat weblog, whose summaries and discussion are good [1,2]. EPO President Brimelow's referral is a reflection of UK case law. In Aerotel [3], Lord Justice Jacob (most senior rank of UK Judge) asked the EPO to clarify its position on patenting software. The second link from the IPKat tells us that an Enlarged Board is at its own discretion able to ignore the referred questions because EPO practice in granting patents for computer-implemented inventions hasn't been inconsistent.