I know I am replying to an old post but I was googling to see if there was an answer to this for me as well and I see this was never really answered. It doesn't matter what you check inside the program, I double and triple checked that this never got re checked, it is definitaly turned off, it seems that every time there is a CCleaner update it re-adds itself to system startup. The average user would not know how to change this. Here is how, though I wish this would just get fixed so I don't have to check this all the time. I am using Windows 7.
*Be careful making changes to system things
start button
type in msconfig
open msconfig.exe
click startup tab
uncheck ccleaner
click ok or apply, you can exit without restart unless you need a reboot then.
