Let me try, since I (think) I'm having the same issue:
I have one iCloud account. I am only logged into that account. When I check my Internet Accounts, iCloud only appears once; when I check the Accounts tab under Preferences in Contacts, iCloud again only appears once. But I have two identical sets of iCloud groups in the Groups pane for Contacts (see below). None of my contacts are duplicated and changes made in one account propagate to the other account. This duplication issue exists for both my macs, but not for my iPhone and not on iCloud.com. I have tried all the basic fixes (bouncing Contacts in iCloud, bouncing all of iCloud, cleaning out the AddressBook data in Application Support). I think it's something in my address book configuration that I haven't cleaned up yet but I don't know what to try next.
For reference, I'm running the latest El Cap release, installed as an upgrade over Yosemite. I've been alternating upgrades and clean installs for several years now, using Migration from Time Machine backups to restore user accounts after clean builds. I think the Migration process is partly to blame here, because I've found files dating back to c. 2005 (my first PowerBook). Thoughts?
