I think if it was a dodgy copy of Windows, you would be getting Activation messages, and "This is not a genuine copy" popups. Windows is pretty much in your face about it if it decides that it isn't legit. I've never known breaking some random component as an anti-piracy measure.

I think Train's suggestion of installing in small batches is a good one, I've had to do that myself in the past, and it often works OK where installing all updates in one go causes problems.