OK just some later news after a bit of hassling around…
I re-compiled root 6 from scratch with the latest CMake distribution and VS 2017 but the same problem remains. Then I uninstalled everything and tried one of the compiled binaries for windows from the webpage, and I still experience the same issue.
Then i reinstalled root 5 (with VS2017 I might add) which works without any problem!
This is specific to root 6, so there is an issue somewhere and is probably not related to my system. The only reason i need root 6 is because i need fftw and root 5 will not compile from source with my configuration correctly no matter how many different versions of cmake and vs studio i try.