I've been using Prepar3d on a clean windows 8 system with no other flight sim. I've had a few issues that I believe were mostly related to how it was installed.
I strongly advise running the Prepar3d setup program in Administrator mode and then going back into the Lockheed Martin/Prepar3d/ directory tree structure and setting the file permissions to Full Control. Then, I also recommend running the Program in Admin Mode during normal use. Seems to help avoid some of the problems others reported.