Top Answer:
Unless a hardcore windows systems hacker comes along, you're not going to get more than partisan comments (which I won't do) and speculation (which is what I'm going to try).
1. File system - You should try the same operations (including the dir) on the same filesystem. I came across this which benchmarks a few filesystems for various parameters.
2. Caching. I one tried to run a compilation on Linux on a ramdisk and found that it was slower than running it on disk thanks to the way the kernel takes care of caching. This is a solid selling point for Linux and might be the reason why the performance is so different.
3. Bad dependency specifications on windows. Maybe the chromium dependency specifications for Windows are not as correct as for Linux. This might result in unnecessary compilations when you make a small change. You might be able to validate this using the same compiler toolchain on Windows.