Well, I actually faced the same problem after I updated to El Capitan. The following did solve the problem.
Go to System Preferences then click on Sign out button. You then must be warned that if you turn off iCloud driver, all documents stored in iCloud will be deleted from your Mac. Do not be concerned since all date is still kept safely from iCloud server. Just go ahead by clicking on "Delete from Mac" button.
After that, restart your Mac, then re-login to your iCloud again. Users will be asked to verify the login request (I verified it from an iPhone).
After all above, your problem should be solved.!