Run the registry permissions repair from my WR v3.5.0 and it will fix it.
SetAcl that I was using before wasnt setting the permissions correctly. I have replaced it with my own and it now restores the permissions correctly and it also fixes this issue. This is a registry permission problem somewhere in the hkey_classes_root and is one of those annoying, poor programming bugs of Microsoft's where if a certain key, even though it does have full access, isnt exactly the way it wants it will bug out.
So lets say a key has Administrators set as the owner instead of System. Even though system has full access to anything administrators do, it will error. Windows 8 app store had this same bug. The start menu in 10 isnt the start menu in explorer, it is actually an App now.
So now in the new version of my Windows Repair the proper defaults get put back and the start menu icons, and right click menu start working again
Shane