Turk13: The trick is to turn off your internet connection. I tried everything; compatibility, run as admin, disable full screen, etc. Nothing worked until I turned off my wifi and disabled my ethernet adapter (Control Panel\All Control Panel Items\Network Connections). I have both a wireless antenna and a hard-wire connection.
My rig:
Windows 10 Pro
i7-6700
16 GB RAM
NVIDIA GTX 970
Bumping this thread because this solved a similar issue I had with the game freezing for 10 seconds at a time whenever saving the game or loading user settings.
Cheers and happy alien hunting.