I had to register an account just to answer this :mad:
Unless your game carries Microsoft branding, Microsoft can't do a damn thing about what software you write for their platform. Laws against monopolies keep them from closing the platform for one. If Microsoft could have the say in what software gets released, then they'd be all over LibreOffice and OpenOffice. The only Microsoft related stuff is the APIs which the licensing they released it under forbids them to control access to, sure they could release a new API version tomorrow that allows them to control it, but then you just keep releasing your software under the old API version. As for the $45,000 patches, that's possibly for XBOX and PS3 which are completely different in terms of who owns what.
How do I know? Because Windows is my primary development platform.
edit:
Microsoft doesn't charge royalties for two reasons:
Developers are the life-blood of Windows. They NEED the developers. Plenty of FOSS alternatives on Linux...
They can't.