When I first saw the results, I was surprised, but not so much that I thought something malevolent was at work. Instead, I viewed the results much like I do with tech review sites. I had inferred Microsoft had gotten some poor dev to hack together a build of the latest revision and email it to the W3C asap. Everyone else just shrugged and pointed to their respective dev builds. Let's not forget certain tech websites don't actually buy all the wonderful products they test. And yet, they use these results to make blanket statements about certain products all the time... I'll be frank, I think factory overclocks and binned chips are just as bad as mixing beta/stable software.
In my opinion, people shouldn't be surprised by Microsoft. It has A TON of good developer muscle. I would imagine everyone who reads Tom's regularly runs Windows. Why? Because Microsoft seriously invested time and money into DirectX and has made it the only serious computer gaming platform. I see no reason why Internet Explorer can't be the best browser in the world. The only real thing in my mind that makes IE an inferior browser is its lack of good security measures. Even then, who knows? I'm sure the devs are perfectly capable of sandboxing IE.