I don't think they have changed anything in September. If they had, there should be more discontinuity in the numbers.
Something happened on the user side that prevented them to be counted to "Windows". It prevented them to be counted to one of the other named OSs. The users counted went from "Windows" to "unknown". The easiest explanation is that those users changed their telemetry settings – stopped browsers and the OS from reporting the correct data.
We don't see it on other statistic services because they have a different metric. Netmarketshare, for instance, was always criticized for counting only corporate users using a specific set of web applications (biasing towards Windows). Those users are unlikely to wiggle their privacy settings.
Now, one can wonder why this is happening, and happening now. There's an easy suspect.