This can be seen with Portable CCleaner, and probably experienced with the installed version.
When CCleaner is first added to a computer its cleaning options are defined solely by :-
defaults built into the executable configuration ; and
defaults in any supplementary Winapp2.ini enhancement.
Upon launch those defaults will be over-written by user changes held in CCleaner.ini
When CCleaner runs it shows which cleaning capabilities are relevant to this computer's software and whether those capabilities are enabled.
If the user changes any default his change is written to CCleaner.ini and preserved in CCleaner.ini.
CCleaner.ini does NOT capture the defaults.
The user MUST modify an option before it is set as an over-ride in CCleaner.ini.
If the default option is not acceptable then correcting it will update CCleaner.ini with a user choice over-ride.
If the default is acceptable then CCleaner.ini is not touched,
and any future change to defaults in CCleaner.exe or Winapp2.ini will not be opposed by CCleaner.ini,
and passwords that were preserved will be (securely) erased,
and confidential data that was being destroyed will be left in open view,
and unwanted junk that was zapped will now waste free space.
I think this is the cause of a complaint a few weeks ago that something important that was being preserved had been deleted as a result of a CCleaner Update.
This also applies to WinApp2.ini - I remember seeing recently strong representations from a User that one of the defaults was dangerous.
A SOLUTION is to double (or triple) click all the options so that your user choice is asserted and written to CCleaner.ini
I WOULD LIKE :-
After User examination he may press a "Global Accept" button that causes ALL the (not)clean check options to be written to CCleaner.ini as a future over-ride ;
PLUS there-after a highly visible indication of ALL new items which have no corresponding CCleaner.ini over-ride.
This should immediately draw attention to any new capability that has not yet been evaluated,
such as a new application that has not previously been detected,
or an old application which has just become subject to a new capability in CCleaner.exe or Winapp2.ini.
I believe all that I have said about CCleaner.ini is probably applicable to HKCU\whichever\whatever for the registry dependant installed versions.
Regards
Alan