I'm a little confused what your argument is, then. You claim that software is not patentable in the EU, but then accept that some companies manage to get software patented in EU countries by writing their patents creatively.
So... software is patentable in the EU, at least in some circumstances. That's the end result, even if technically it's not allowed.
Unless these patents in question don't actually cover video codec software, which it seems they do?
The ultimate test, of course, is if these patents would stand up in court. But it seems no one has challenged them? Which indicates to me that either a) people believes they would hold up in court, and so they don't try to challenge them, or b) no one is sure, and is afraid to find out. Either outcome has the end result of "software can be patented in the EU sometimes".