Windows drops the regkeys into the wrong location to provide 32-bit compatibility. (HKEY_CLASSES_ROOT\Wow6432Node\CLSID\{645FF040-5081-101B-9F08-00AA002F954E}\Shell)
Use this file to correct the registration issue.
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Windows Registry Editor Version 5.00
[HKEY_CLASSES_ROOT\CLSID\{645FF040-5081-101B-9F08-00AA002F954E}\Shell]
[HKEY_CLASSES_ROOT\CLSID\{645FF040-5081-101B-9F08-00AA002F954E}\Shell\Open CCleaner...]
[HKEY_CLASSES_ROOT\CLSID\{645FF040-5081-101B-9F08-00AA002F954E}\Shell\Open CCleaner...\command]
@="C:\\Program Files (x86)\\CCleaner\\CCleaner.exe"
[HKEY_CLASSES_ROOT\CLSID\{645FF040-5081-101B-9F08-00AA002F954E}\Shell\Run CCleaner]
[HKEY_CLASSES_ROOT\CLSID\{645FF040-5081-101B-9F08-00AA002F954E}\Shell\Run CCleaner\command]
@="C:\\Program Files (x86)\\CCleaner\\CCleaner.exe /AUTO"