Auto will clean anything you have checked off in the cleaning section. Don't know what's causing the volume change but the winrar can be found in the applications tab. Auto won't run registry integrity section, but MRU are usually cleaned in the cleaning section so it's there that winrar is being cleaned.
WinRAR MRU can be unticked in CCleaner so that it doesn't clean it. As for the system volume being changed I don't know, other than if you use a downloaded winapp2.ini file move it out of the CCleaner folder to see if that stops the behaviour from happening again.