Hi,
running xp sp2
CCleaner v2.01.507
Run (in Start Menu) ie. HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\RunMRU, is still cleaned if Internet Explorer>History is checked, regardless of whether Run (in Start Menu) is checked.
Uncheck Internet Explorer>History and then the RunMRU is only cleaned if Run (in Start Menu) is checked.
Obviously something that still needs fixing.