As for PCT. Patents enter the national or regional phase and get examined against the local patent law. Some countries may be inclined to rubber stamp already granted patents (saving time and money). Certainly USA searches for PCT used to be the only ones that were guaranteed _not_ to be thorough!
(3) Paragraph 2 shall exclude the patentability of the subject-matter or activities referred to therein only to the extent to which a European patent application or European patent relates to such subject‑matter or activities as such (emphasis added)
This is where I imagine much of the confusion lies. My interpretation combined with a brief search on google seems to indicate that software could make its way into patentable subject matter if it's a subset of a larger system, but not if its the sole "invention" claimed in the patent.
In other words, if you have a hardware device running embedded software, you could patent the device, including in it "programs for computers." Thus, Art 52 doesn't mean that all inventions including computer software are, as a matter of law, not patentable.
There have been several instances, however, where large American companies have tried to get Europe to allow software patents. Luckily so far all of these have been blocked:
Nonsense. We have software patents in Europe too.
See http://en.wikipedia.org/wiki/Software_patents_under_the_Euro...
Thankfully, Art. 52 of the European Patent Convention is pretty sensible in that it does not regard discoveries, scientific theories and mathematical methods, aesthetic creations, and "schemes, rules and methods for performing mental acts, playing games or doing business, and programs for computers" as patentable subject matter.[1]
[1] http://www.epo.org/law-practice/legal-texts/html/epc/2010/e/...