I only ask because I just ran the program "autoruns" and it was picking up all my disabled startup items as enabled. Is this because ccleaner itself keeps disabling the items at every startup manually and there is not some global startup disablement location that ccleaner and autoruns both have access to see?
What CCleaner can disable can usually also be re-enabled using MSConfig via Start-Run. Note: This excludes web browser addons/extensions.
If you disable something using CCleaner it will not magically re-enable it should you decide to uninstall CCleaner. Either remember to re-enable it, or use MSConfig to re-enable if CCleaner is no longer installed.