Welcome to the wild and wonderful world of Windows' permissions
Do this http://forums.adobe.com/thread/969395 (Encore AND PPro) to use the "Run as Administrator" option... which fixes most permission problems
I ran CS5.5 on Win 7 then, after upgrade, on Win 8 with no permissions problems.
CS6 Encore not only requires Run as Administrator, but stops at unpredictable times during a project.
So, prima facie,the problem is with CS6 Encore.
ie CS5.5 Encore runs fine on my system with Win 8. CS6 Encore crashes on the exact same system.
What do I do?