Hashrate linux vs. windows

I just started my mining adventure yesterday, and after trying solo mining i quickly realized it was not the way to go. So i decided to try pool mining and went for the thrustworthy looking zcash.flypool.org

So first i downloaded and compiled their nheqminer for Linux CPU mining and let it run overnight. Then i tried their windows CPU miner on the same machine. I tried compiling but it failed due to difference in VC SDK, so i went for the quick solution and just downloaded the executable (I'm actually a little scared to have done that).

The resulting hashrate difference is rather stunning and i'm a little puzzled why that is. The only difference i can think of is that windows runs on an SSD and linux on a HDD, but can this really make such a difference?

Processor: i5-6600K normal clock rate of 3.5 GHz

Linux mint 18: 10 Sol/s
Windows 10: 25 Sol/s

Any ideas?

Have you tried mining with Linux since then?