The hive [HKEY_CURRENT_USER] is subset of [HKEY_USERS\S-1-5-xxxx] that details out the profile of the current user;
The hive [HKEY_CURRENT_CONFIG] is a subset of [HKEY_LOCAL_MACHINE\Config] that details the current configuration;
The hive [HKEY_CLASSES_ROOT] is subset of [HKEY_LOCAL_MACHINE\Software\Classes] with class definitions.
Registry First Aid scans only one hive of these doubled keys. For instance, it scans [HKEY_LOCAL_MACHINE\Software\Classes] and doesn't [HKEY_CLASSES_ROOT]. All corrections applied to only one set will be reflected to another set too.
To avoid deleting of registry entries that are necessary for some programs Registry First Aid has several excluded lists. These excluded lists contain registry entries that should not be deleted or changed. Other registry cleaners may not have that and will find and remove important registry keys.
Registry First Aid has the Excluded Registry Strings List. Into this list, the user can add drive letters of paths to ignore when scanning the registry. For example, if you do not want to remove registry references to files on a CD-ROM that currently is not in a drive or on a removable drive then you can add their drive letters into the this excluded list. Many registry cleaners do not have this type of list and look for all references to all drives. And while scanning you may even see the "Please insert a disk into drive X: (Abort, Retry, Ignore)" message.