From what I have gathered, CCleaner checks
HKCU\Software\Microsoft\Windows\CurrentVersion\Run
and
HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
as well as the user Startup directories for the Startup Tool
The following locations contain single programs that are also executed during logon...
HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon\Shell
HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon\Userinit
HKLM\System\CurrentControlSet\Control\Terminal Server\Wds\rdpwd\StartupPrograms
These are slightly more system critical entries, so if they are added, they should only appear if an advanced option for them is checked.