When you use Registry.SetString(key,value)
or any other Registry.Set*
you're setting in fact this value on user profile:
Sitecore.Context.User.Profile[key] = value;
Clearing the cache will not help you here. Even if you clear the value in cache, it will still be set on the profile and loaded from there if needed.
EDIT
I've written a blog post describing how you can work with Sitecore Registry and with simple Sitecore Registry Editor application.