It seems to me that using CCleaner.exe /AUTO runs the stuff in Cleaner/Windows but not the stuff in Cleaner/Applications. Can you please confirm that this is accurate and let me know if there is some way to run the /Applications items as well?
Thanks,
JCLEANER
It cleans both Windows and Applications but doesn't touch the Registry cleaner for obvious reasons. To confirm run via CLI and then double click on the icon in the task and watch the CCleaner progress, if your running Opera as a browser and you have this selected to be clean you will see your porfile being cleaned (as an example!)