Not sure if its any help, but I'm running KSP 64 bit on Windows 7 64bit, using Stock Visual Enhancements / EVE and Scatterer. With Kopernicus, getting the black sky on the launchpad, (enabling stock atmo brings it back, but scatterer won't load till you hit 17km above surface). Removed Kopernicus, and everything works flawlessly. The Alt+Tab thing seems to cause scatterer to re-render, causes a slight pause, but resumes normal operations afterwards.
EDIT: Default DX9 load