I know quite well a patent examiner there; there is a lot of politics and incompetence in appointing people and a lot of pressure to accept most of the patents they receive, if I understood correctly part of the reason is politics (if you refuse, even stupid patents, influential people will get upset) and part is the idea to have as many patents as possible as a measure of European creativity and innovation and ... bla-bla. Universities and research institutes are measured by the number of patents and if they don't invent something good, they will patent something stupid just to get the numbers right.

The reasoning is that individual states have Opinions about the validity of software patents and they're going to keep issuing them until somebody with the proper authority clarifies that the law means what the law says, although as far as I can tell none have actually been successfully enforced.