I've been thinking about MS's position on this and it is pretty strange. Typically, if someone who is violating one of your patents, the first thing you do is inform them of the patent and explain to them how they are violating it. That way, they are put on notice and if they continue to infringe the patent you can obtain treble damages for willful infringement. Here though, MS is doing nothing of the kind. They are not even identifying what parts of the Linux kernel constitute infringements, so it is not possible for Linux to stop infringing.
I am not an expert in this area of the law, but it seems to me that Linux might be able assert a defense of waiver. Here, MS says its patents are being infringed by Linux - doesn't identify them -- and doesn't intiate legal action against Linux. The net effect is that MS is letting Linux violate its patents without taking action to stop the infringements. That sounds like a waiver of the patents claims.