MS didn't understand the technology. They went to I4i to understand it. I4i cooperated because MS came in concert with US intelligence and US intelligence was wanting to understand how they could search documents quickly after 9/11. That makes the technology, at that time, both non-obvious and novel to MS, the US government, and most likely the rest of the commercial software world, as they hadn't been able to find anyone who did what I4i was capable of doing. Just because, years later, you think you understand the patent and claim you can think of may applications that violate the patent doesn't invalidate the patent. It had to be innovative/novel/non-obvious then, not now.
Here's a link to give more background.
http://www.theglobeandmail.com/news/national/the-biblical-vengeance-of-i4i/article1253054/