The difference is that I use Apache, instead of IIS, on my Windows servers. I gave up on IIS years ago because of endless problems. WP Super Cache 1.1 runs fine under Windows with Apache. Apache is free, easy to install, more configurable, more reliable, faster, and runs most website code developed under Linux without problems.
If there is some compelling need for IIS, both web servers will run compatibly under the same Windows installation if they are configured to use different IP Addresses or Port Numbers and a router is used to route incoming traffic.