It's difficult to pick through the whole issue, but here's what I get from it. The GPLv3 has wording that makes it clear that you must also provide rights to any patents you use in the software when you distribute it under that license. It's a way to avoid patent encumbrance: If you won't give it away to everyone, then don't give it away at all.
Microsoft doesn't believe that distributing support certificates for Linux through partners like Novell makes them beholden to the any aspect of the GPL -- no more so than, say, someone who does Linux tech support for a living. Therefore, they have no reason to believe the GPLv3 is binding to them if they offer vouchers for products distributed under that license. Since the vouchers don't expire, it's theoretically possible that someone could cash one of them in for a GPLv3 item. To that end, Novell will apparently do the actual support for any GPLv3 products and leave Microsoft entirely out of the loop. (The other deals brokered with Xandros and Linspire are apparently going to be handled the same way. One major Linux player who's already openly blown Microsoft off in the patent department is Red Hat, although they're still interested in talking about pure interoperability issues.)
If there are patent violations, people say, why not just cite them so they can be fixed? Microsoft sees the whole thing differently: For them, it's not about spot-fixing infringing patents as they come up, but creating a permanent IP indemnity between them and a given Linux vendor whenever possible. That way, they're dealing with a given vendor and not with the open-source movement as a whole, a war that anyone here knows is inherently unwinnable. As a friend of mine put it: In any fight between you and the world, bet on the world.
That's really what this whole thing seems to be about. Microsoft wants to constrain its struggles with Linux to specific playing fields (i.e., vendors). The introduction of the GPLv3 has the potential to unseat all that. Even if the Linux kernel itself isn't relicensed under those terms, many of the user applications that go with a given Linux distribution -- including Novell's own SLES -- may well be released in v3 versions. When that happens, the only thing Microsoft can do is insist that any vouchers they make available in the future under the provisions of this deal can't be redeemed for GPLv3 material -- and a good deal of their work to constrain the playing field will probably just vanish.
I've long thought that the best way for Microsoft to compete with open source in any form is just to make the best product it possibly can. Forget about arcane patent cross-licensing -- build a great piece of software, make it available at a good price, make it interoperate well, and people will come for it. The way licensing deals like this can be subverted is just further proof that they need to stay on their own playing field.