I have the same problem but only so far with a Sparkfun M0 mini board. I also bought an Adafruit Feather M0 and it works fine, even if I tell the Arduino IDE that I am using the sparkfun board it will download fine for the Feather M0.
The sparkfun board only uploads fast when I put some load on my laptops CPU, like playing a youtube video.
As far as I can tell, this is an issue with the Sparkfun version of the SAM_BA bootloader and nothing to do with Windows but I am about to get a second Sparkfun M0 board to check this out some more.