That, apparently, is the reason the release of GPLv3 has been delayed. The Free Software Foundation wants to ensure that verbiage in GPLv3 explicitly prevents arrangements wherein Microsoft signs a patent waiver with customers of a particular company (in this case, Novell). That, apparently, is not disallowed by the terms of GPLv2, according to Richard Stallman.
Assuming they figure out acceptable verbiage (which I have no doubt the FSF will), this means that the only way GPLv3 software could use patented IP is if the owners of that IP grant a global waiver to all users of a particular open source product. Though that does on occasion happen (IBM and Sun have done so, among others), it does carry risks - namely, that the granter of the waiver can't use those patents in future against users of a waivered product who choose to sue the granter of the waiver over IP they own (now say that fast three times).
That certainly matters to a company like Microsoft, who just stepped on an Alcatel-planted patent landmine, resulting in medical bills in the 1.5 billion range (pending appeal, or the judge reducing the size of the fine). Granted, that should be a lesson to companies like Microsoft that software patents aren't such a wonderful thing (I am certainly of that opinion), but they exist today, and if you want to mount a counterattack, you need to have your patent weaponry in good working order and able to be launched against anyone. Part of Microsoft's Alcatel counterattack is a suit using patents Microsoft holds that aims to block import of certain Alcatel products. Similarly, IBM, in its defense against SCO, countersued using a number of patents they own, one of which appears to be a patent on the common menu user interface convention.
Terms in the GPLv3 that block deals like the one between Microsoft and Novell mean users of a GPLv3 product will have to a) convince companies to grant patent waivers (which carries risks), b) avoid all patented IP (not so easy given how broadly worded patents can be; Microsoft has teams of people dedicated to researching IP in their products and they still got hit by Alcatel), or c) live with the risk. Truth be told, the odds of Microsoft making a full-on Alcatel-style patent assault on open source products is low given the nuclear fallout from such an attack, but there are red lines. For instance, I don't think Microsoft would take kindly to a GPLv3 implementation of WMA, as an example, as that is something they license.
Whatever the case, the FSF gears continue to grind away at the potential relevance of the GPLv3, creating a license that makes it even harder for proprietary software and patented IP to interoperate with GPLed software. Even though I work for Microsoft, it IS my problem as someone who appreciates the strengths of community-developed software and desperately hopes that Microsoft could find ways to use more of it. Making the two streams of innovation mingle benefits the software art, which is why it is so exasperating to see certain proponents of one those streams loudly continue their advocacy of the software equivalent of apartheid.