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Every time I use CCleaner to clean my system, regardless to what settings I set up (as far as I could find), it purges my Start Menu most used applications list (the main (lefrmost) column of the Start Menu). Is it possible to disable this behaviour? I only want it to delete temporary files.

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Just disable all Windows Explorer options specifically Run(in Start Menu) and Start Menu Shortcuts and Desktop Shortcuts and it should solve your problem. You could also disable EVERYTHING except Temporary Files if you want and it would also solve your problem.

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