Most software patents are nothing more than an idea. A reasonably detailed idea in most cases, but it's just a specification of a process. Have you read many? Sometimes you get a flowchart but often not even that. The 'inventor' may well have made an actual implementation but it's almost never included in the patent (see the above discussion about including the source in patents). Also remember that it usually consists of a basic idea modified/built-on in many separate claims, and the validity of each claim must be challenged separately. You have to show that _all_ of them are invalid to fully invalidate the patent.
But still, whether it 'works' (how exactly would you define that?), really isn't part of the legal definition, and thus isn't something you can usefully challenge on, SFAIK.
We do have an actual (european) patent agent on LWN these days who might be able to give chapter and verse on this point.