I don't know if this scans yet but i think it be a good idea to delete Obselete files left behind from recently uninstalled programs like C:\Program Files\ area of obselete applications and C:\Documents and Settings\%user%\Application Data\
Data left behind from apps.
When you run the registry cleaner, if you fix all isssues then you load up skype after it will run a repair wizard on skype trying to repair skype.
It seems CCleaner is deleting something precious about skype.