Hi FF8,
This options will not effect your registry! Maybe files, folders, entries are shared with other aplications!?!
Then, in my discretion, CCleaner can't touch this entries.
Uninstalled with programm Uninstaller, Windows Uninstaller or CCleaner Uninstaller?
More Info about your Registry, System and so on may help, normally some leavings will not slow down or impair your system. Sometimes, this vestige is needed. (No way, talking about binding effect without detailed system information!)
Deleting registry entries manually... Bad idea, doing it with levity!
That stuff that's left... If you know what you are doing, delete it - otherwise, if that stuff don't derogate your system, let it live!
If you are able to send more info (system, programms, your Procedures, registry prints...) maybe the forum users will solve your problem!
Greetz, ZikZak
p.s. If a registry folder is (absolutely) empty, just don't take care of it!
p.p.s. I'm not a win-reg-pro - just wrote my first impression!!!!