CCleaner version 2.01.507
I don't know if I've come across a registry exclusion bug or limitation.
What I was trying to exclude is listed in the code, however each entry seems too long and I can't tick the OK button to have it inputted because it's greyed out. Shorter entries are however allowed.
I know it's somewhat meaningless to exclude StartMenu2 entries, it's just that it gets old seeing them listed in the invalid registry data everytime since the folder locations actually exist.
HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\Audio-ToolsHKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\Copy Drive To Drive ScriptsHKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\Copy Files and FoldersHKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\HTML Document TemplatesHKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\System ToolsHKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\System Tools\Clean System Registry EntriesHKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\System Tools\File EditHKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MenuOrder\Start Menu2\Programs\System Tools\Junk File Cleaners
Example, screenshot of one entry: