At the time set in Options>Scheduling, CCleaner runs the task "CCleanerClean" in Task Scheduler. This task is set to use the admin user account and only when the (admin) user is logged in. For me at least, I find therefore that when the only account I am logged into is a non-admin account, then C:\Windows\Temp will not get cleaned (and I assume any other items set to be cleaned by Health Check or Custom Clean, but I did not test this). I tested this on 2 different PCs, both with same Windows build, same CCleaner version, same security permissions on C:\Windows\Temp. I also re-installed Windows 10 on a blank drive then installed CCleaner. Every time I found the task will run only when the admin user account is logged on.
You can change the task to use a non-admin account or change it so that will run when the admin user is not logged in. Then C:\Windows\Temp will be cleaned. I tested that this change will persist on a reboot and it will. It will also persist if you change any of CCleaner's options, except for the options in Options>Scheduling (either as the admin user or as the non-admin user). If you change the time that the cleaning is done in Options>Scheduling, CCleaner will change the task back to use the admin user account and run only when the admin user is logged in.