Reset the entire registry permissions to defaults
Here is the detailed instruction on resetting the permissions for the whole registry. This was posted by Ken Zhao of Microsoft.
1. Download and install
SubInACL
2. Create a file named reset.cmd in C:\Program Files\Windows Resource
Kits\Tools folder.
3. Edit the reset.cmd file with the following content.
subinacl /subkeyreg HKEY_LOCAL_MACHINE /grant=administrators=f
subinacl /subkeyreg HKEY_CURRENT_USER /grant=administrators=f
subinacl /subkeyreg HKEY_CLASSES_ROOT /grant=administrators=f
subinacl /subdirectories %SystemDrive% /grant=administrators=f
subinacl /subkeyreg HKEY_LOCAL_MACHINE /grant=system=f
subinacl /subkeyreg HKEY_CURRENT_USER /grant=system=f
subinacl /subkeyreg HKEY_CLASSES_ROOT /grant=system=f
subinacl /subdirectories %SystemDrive% /grant=system=f
4. Enter into CMD prompt.
5. Enter the following commands one at a time and click Enter.
cdcd "C:\Program Files\Windows Resource Kits\Tools"
reset.cmd
6. After a few minutes by processing subinacl, the permission will be reset.