Please note that I also am seeing this behavior were my CCleaner is launched at startup and runs minimized to startup tray. But, at a point it seems to disappear from the tray. I also check Task Manager and CCleaner is no longer running. I launch again and after a while it stops again. I checked the settings recommended by support earlier:
Options > Settings > Run CCleaner when the computer starts
Options > Smart Cleaning
Options > Advanced > Close program after a Custom Clean
Options > Advanced > Minimize to System Tray
It is set like this.