Paul Allen owns the entire Vulcan group. One division of that, Vulcan Real Estate, owns and is developing all the brand new buildings on South Lake Union in Seattle that Amazon is now leasing out for their new campus.
Why waiting so long ? There should be a prescription on this type of claims. This technology is used in a very visible way for years now. So they could not ignore it and thus implicitly permitted to use it.
If they didn't knew they had these patents, how could the other company know ?
This type of pattent 'mines' will have the consequence to scare to death companies. Foreign companies will stay away of US just to avoid the risk to step on such mine. And US companies may move their business in countries with much less risks (i.e. europe, Asia).
If I had to guess, it's because he doesn't want to sue a company he has a stake in. That's like suing yourself. Patent and intellectual property copyright is a funny thing; the owner can enforce (or try to get it enforced) when they feel like it. They usually let it go when it's to their benefit.
It's obvious why - nobody said patents were "fair". The patent holder has his own discretion.
He's not suing microsoft because he'd be shooting himself in the foot. He might have a deal with them to license it, or he may just be letting it slide (he can always sue them later). Same with google.
He's under no obligation to enforce his patents - it's up to him.