AFAIK, the servers itself are all-microsoft,
most brobably netcraft.com is confused by load-balancers (akamai or something similar)
The "Linux" servers are Akamai's.
This has been going on since windows NT launched (as in, that's when people first found out). They just outsource a lot of their website load to external hosts who run Linux.
Akamai isn't Msft they just have subdomains pointed to it