In my case (WinXP SP2, CCleaner 1.40, Skype 3.2) following keys are concerned:
"HKEY_CLASSES_ROOT\{327C8820-8DED-4BD2-A7F6-D07B9DD5698F}"
"HKEY_CLASSES_ROOT\{A4B980AE-402C-4EA4-9D1B-83A7A8CEE7E4}"
I think, the problem is they are empty so they seem useless. But when starting, Skype seems to check whether these keys are here. If not, Windows Installer starts with this message: "Please wait while Windows configures Skype."
This problem started with Skype 3.2. I don't think I installed a new version of CCleaner when this occurred for the first time, but I'm not sure anymore.
Tobias