@Bazza

In a nutshell it is arguable that GPLv2 allows for individual patent protection agreements* whereas GPLv3 does not.

So under v2 TomTom and MS are free to agree a deal whereby MS promise not to sue TomTom or their customers )explicitly of the TomTom products agreed) regarding FAT, however this agreement does not remove the threat of suing any non-TomTom party for breach of the FAT patents.

Under v3 any agreement not to sue over FAT would explicitly and irrevocably pass on to any other users of FAT using products (TomTom couls only sign this agreement if MS agreed to waive suing rights to all GPL3 parties).

Thus MS would have to decide whether to actually sue TomTom, with at least amicus backing from all other GPLv3 / FAT users or let it go. If they sue over FAT there is a very good chance they will lose (10 minutes on Google shows you plenty of prior art and obviousness). However as it stands MS have "won" a FAT patent battle in this instance and after a while they would be able to claim enough "victories" that many courts would find in their favour based simply on that.